Vercingetorix now withdrew to Gergovia, the capital of his own tribe, which he was eager to defend. Caesar arrived as the weather warmed, and fodder finally became available, which somewhat eased supply issues. As usual, Caesar promptly set about building a fortification for the Romans. He captured territory closer to the oppidum.

The loyalty of the Aedui to Rome was not entirely stable. Caesar suggests in his writing that Aeudui leaders were both bribed gold and sent misinformation by emissaries of Vercingetorix. Caesar had agreed with the Aedui that 10,000 men would protect his line of supplies. Vercingetorix convinced the chief, Convictolitavis, who had been made chief of the tribe by Caesar, to order the same men to join him upon their arrival at the oppidum. They attacked the Romans who were accompanying their supply train, leaving Caesar in an embarrassing position. His rations threatened, Caesar took four legions from the siege, surrounded the Aedui army, and defeated it. The pro-Roman faction retook control of the Aedui leadership, and Caesar returned to Gergovia with 10,000 pro-Roman Aedui horsemen. The two legions that he had left to continue the siege had been hard-pressed to keep Vercingetorix's much larger force at bay.

Caesar realized that his siege would fail unless he could get Vercingetorix off the high ground. He used one legion as a decoy while the rest moved onto better ground, capturing three Gallic camps in the process. He then ordered a general retreat to lure Vercingetorix off the high ground. However, the order was not heard by most of Caesar's force. Instead, spurred on by the ease with which they captured the camps, they pressed on toward the town and mounted a direct assault on it, exhausting themselves.

Caesar's work records 46 centurions and 700 legionaries as losses. Modern historians are skeptical; the depiction of the battle as a rout, and one where there were 20,000-40,000 allied Roman soldiers deployed, leads to suspicion that Caesar was downplaying the casualty figures, even if his figures were excluding losses among allied auxiliaries. Given his losses, Caesar ordered a retreat. In the wake of the battle, Caesar lifted his siege and retreated from the Arverni lands northeastwards in the direction of Aedui territory. Vercingetorix pursued Caesar's army, intent on destroying it. Meanwhile, Labienus had finished his campaign in the north and marched back to Agendicum, Caesar's base in the centre of Gaul. After linking up with Labienus's corps, Caesar marched his united army from Agendicum to confront Vercingetorix's victorious army. The two armies met at the Vingeanne, Caesar won the subsequent battle.