Leverkusen looked comfortable until Timo Werner suddenly smashed in Leipzig’s second just after the hour mark.
Emil Forsberg then put Leipzig in front from the penalty spot before Cunha secured the three points with a splendid lob seven minutes from time.
Leipzig are three points ahead of fourth-placed Eintracht Frankfurt, who snatched a late 2-1 win at Schalke.
Ante Rebic rounded Schalke goalkeeper Alexander Nuebel on 13 minutes to put Frankfurt ahead, but Suat Serdar levelled the scores with his second goal in two games.
Yet Frankfurt were awarded an injury-time penalty by VAR and Luka Jovic fired in the winner.
Schalke remain five points clear of the bottom three after Nuremberg and Stuttgart shared the points in a relegation showdown.
Matheus Pereira’s opener for Nuremberg came against the run of play just before half-time. Stuttgart’s Ozcan Kabak then scored a controversial equaliser, given by VAR despite an apparent offside in the build-up.
The equaliser keeps Stuttgart four points ahead of Nuremberg in the relegation play-off place.
Relegation seems all but certain for Hanover, meanwhile, after they suffered a 3-1 defeat to local rivals Wolfsburg.
Hanover had an early penalty appeal turned down, but Henrik Weydandt broke free on the counter-attack to slide in the opener after half an hour.
Their lead lasted all of 100 seconds, a Renato Steffen header bringing Wolfsburg level.
Steffen scored again after half-time, and Jerome Roussillon added a third late on to seal the win and push Hanover further towards the drop.
Elsewhere, Benito Raman continued his excellent recent form with a brace for Fortuna Duesseldorf in their 2-1 win over Hertha Berlin.
Hertha’s Marko Grujic cancelled out Raman’s first-half opener, but the Belgian striker scored again after the break to secure three points and move Duesseldorf a step closer to safety.
West Ham United have confirmed the signing of Mexican striker Javier Hernandez from Bayer Leverkusen for a fee of £16million.
The 29-year-old former Manchester United and Real Madrid star put pen to paper on a three-year deal on Monday afternoon and will join Slaven Bilic and his new team-mates at their pre-season training camp in Germany.
Hernandez, who became Mexico’s all-time leading goalscorer earlier this year, is more commonly known to fans as ‘Chicharito’ – the name he will sport on the back of his 2017/18 West Ham United shirt.
“I am very happy to join West Ham United,” he told the club’s website. “For me, the Premier League is the best league in the world and when the opportunity came, I was desperate to sign for this club.”
“It was not a difficult decision, West Ham is a historic club and very ambitious; this summer you can see with the players signed that they are looking to have a very good season.
“I’ve had three fantastic years playing in Spain and Germany, but England was really the first big chapter in my career and I am so happy to be back. I am desperate for the season to start and to help the team achieve all their objectives,” he added.
Real Madrid Coach, Zinedine Zidane says the team will not take anything for granted as the defending champions target their third win in Tuesday night’s UEFA Champions League clash against Sporting Lisbon.
Real Madrid trail Borussia Dortmund with two points in Group F after four games while sporting are third in the group with just one victory.
Real beat Atletico Madrid 3-0 last Saturday in the La Liga but Zidane anticipates a very difficult match against Sporting.
Sporting Coach, Jorge Jesus acknowledged Real Madrid’s quality, but says if his team perform the way they did in Madrid, losing just 2-1, the dream stays alive.
Leicester City can make sure of their place in the knockout stage of the UEFA Champions League on Tuesday if they beat Club Brugge at the King Power Stadium.
Meanwhile, Tottenham Hotspur travel to AS Monaco knowing anything less than a win will see them fail to progress if Bayer Leverkusen beat CSKA Moscow.
Elsewhere, Sevilla and Juventus clash at the top of Group H, while Borussia Dortmund take on Legia Warsaw.
Liverpool have qualified for the Europa League semi-finals with a dramatic fight back to defeat Borussia Dortmund 4-3 at Anfield.
Goals from Origi, Coutinho, Sakho and Lovren helped Klopp triumph in the dying minutes of the game against his former club on Thursday night.
Two quick goals by Henrikh Mkhitaryan in the fifth minute and Pierre-Emerick Aubameyang in the ninth minute half had left Liverpool shocked and on the verge of exit without a fight.
Pressure mounted for the fans as the setback was followed by series of missed chances that left the Anfield faithful frustrated.
The second half started well for Liverpool and the early pressure paid off in the 48th minute through Origi but just when Liverpool thought they were launching a comeback, Marco Reus silenced the home fans with a lovely finish, which left Klopp visibly furious.
Two goals down and three away goals already for Dortmund with less than 30 minutes to play, Liverpool needed three goals without conceding any more goals to win on aggregate, having drawn the first leg 1-1 in Germany.
They made it 3-4 on aggregate in the 66th minute after James Milner played a one-two with Coutinho on the edge of the box, with the Brazilian star guiding home a great strike.
The Brazilian turned the provider of the equalizer in the 77th minutes as he whipped a corner in from the left-hand side with Sturridge managing to do enough to let the ball run past him at the near post!
Former PSG centre-back, Mamadou Sakho was quickest to react and turned home a close-range finish to make it 4-4 on aggregate.
Anfield went wild and they could only pray a complete miracle. One more goal and Liverpool would be in the semis. Both coaches made changes to make the best of the final minutes of the game.
There were four minutes of stoppage time and the pressure got to Schmelzer who picked up a yellow card for petulance, with Dortmund’s tempers flaring after a free-kick was awarded to Liverpool.
The Reds, however, maintained focus and the free-kick was taken short by Milner to Sturridge, with the latter then feeding the former to the right byline. He hung up a lovely cross, with Lovren rising highest at the back post to guide home a thumping header.
It was the 91st minutes and Liverpool had done the unthinkable; fighting back from being 1-3 down to defeat Dortmund 4-3 and qualifying for the semi-final 5-4 on aggregate.
This could go down as one of the greatest nights in Europa League history.
Thursday night ended in disappointment for two English teams, Tottenham Hotspur and Manchester United playing away in the Europa League.
Manchester United lost to Liverpool 2-0 at Anfield in their first meeting in Europe with goals from Daniel Sturridge and Roberto Firmino.
The hosts made the breakthrough in the first half when Daniel Sturridge beat David De Gea from the penalty spot after Nathaniel Clyne was brought down by Memphis Depay.
Liverpool midfielders Adam Lallana and Philippe Coutinho wasted great opportunities to double the home side’s lead before half-time.
However, Roberto Firmino handed the Reds a commanding 2-0 first-leg lead at Anfield after a close-range finish with 17 minutes remaining of the first leg.
Tottenham were shocked by in-form Borrusia Dortmund 3-0 in Germany.
Manchester United and Arsenal target Pierre-Emerick Aubameyang gave the Germans a first-half lead. Marco Reus hit two after the break to make the Germans the favourites to clinch a place in the quarter-finals in second leg.
In other Europa League round of 16 first leg matches played on Thursday night, Swiss Side Basel played a goalless draw with Spanish club Sevilla while Turkish giants Fenerbache beat Portugal’s Sporting Braga 1-0.
Ukrainian power house Shakhtar Donetsk beat Anderlecht of Belgium 3-1 and Athletic Bilbao beat Valencia 1-0 in an all-Spanish encounter,
Sparta Prague played a 1-1 draw with Ogenyi Onazi’s Lazio while Villareal beat Bayer Leverkusen 2-0 at the Estadio El Madrigal.