"The Shamsi base was more of a maintenance and refuelling base for the drones, while most of the operations are conducted from across the border," he said.
"Technically speaking, yes, the vacation of this base should have an impact on the drone operations, but it remains to be seen as to how big an impact this would be."
The source said the United States had at least two other bases in Afghanistan it could use.
The last US personnel left the base at about 12:15 p.m., according to a senior security official who requested anonymity because he was not authorised to speak to the media.
Twenty-one cargo flights in the last 10 days helped with the evacuation. Pakistani security forces now control the base.
Pakistanis saw the US departure as a significant victory.
"It's a big move politically, and does show that we are asserting ourselves and won't tolerate any such acts any more," the senior military source said.
"It also shows that the military as well as the government are on the same note on this issue, and so I will call it a significant move to get the base vacated."
Prime Minister Yusuf Raza Gilani, in an interview with the BBC, said Pakistan could take further retaliatory action, including possibly closing its airspace to the United States.