The Egyptians had set up camp in a strong position along the Nile, and were accompanied by a fleet. Caesar arrived shortly afterwards, before Ptolemy could attack Mithridates' army. Caesar and Mithridates met 7 miles from Ptolemy's position. In order to reach the Egyptian camp they had to ford a small river. Ptolemy sent a detachment of cavalry and light infantry to stop them from crossing the river. Unfortunately for the Egyptians, Caesar had sent his Gallic and Germanic cavalry to ford the river ahead of the main army. They had crossed undetected. When Caesar arrived he had his men make makeshift bridges across the river and had his army charge the Egyptians. As they did the Gallic and Germanic forces appeared and charged into the Egyptian flank and rear. The Egyptians broke and fled back to Ptolemy's camp, with many fleeing by boat.

Egypt was now in the hands of Caesar, who then lifted the Siege of Alexandria and placed Cleopatra on the throne as co-ruler with another of her brothers, the twelve-year old Ptolemy XIV. Caesar then uncharacteristically lingered in Egypt until April, enjoying a liaison of about two months with the youthful queen before departing to resume his civil war.

News of a crisis in Asia persuaded Caesar to leave Egypt in the middle of 47 BCE, at which time sources suggest Cleopatra was already pregnant. He left behind three legions under the command of a son of one of his freedmen to secure Cleopatra's rule. Cleopatra likely bore a child, which she called "Ptolemy Caesar" and which the Alexandrians called "Caesarion", in late June. Caesar believed that the child was his, as he allowed use of the name.