From the help:
"Winning the War
The war is won when any country is reduced to one field. At that time, the arena is reset, a different terrain is rotated in with the country territories randomly set, and a perk point bonus is awarded to players that have been in the winning country for a minimum of 12 hours prior to the end of the war."
I have received war-winning perks while in the tower, so I know that you do not have to be in a vehicle/aircraft at the time of the victory. I believe that the "winning country" is defined as the country that has the most fields at the reset.
