The M23 rebels boarded trucks and headed out of the city, 11 days after seizing it from government troops, backed by UN peacekeepers.
The deal calls for the rebels to withdraw towards the town of Kibumba.
The M23 rebels deserted from the army in April, with some 500,000 people fleeing their homes in the ensuing unrest.
Kieran Dwyer, spokesman for the U.N. Department of Peacekeeping Operations in New York, said the U.N. peacekeeping mission in Congo confirmed the pullout was completed.
“The M23 has today withdrawn from Goma city in eastern DR Congo,” he said in a statement. “MONUSCO mobilized 17 rapid reaction units in the city throughout the day to monitor the M23 withdrawal which took place in a largely orderly manner.”