Federer moved level with Novak Djokovic's tally at Indian Wells by producing a mesmerising performance to claim his 25th ATP Masters 1000 crown and 90th overall tournament win of his career.
The Australian Open champion barely gave his fellow Swiss a look-in with an awesome serving display and was at his classy best as he won 6-4 7-5 on a glorious day in California.
Evergreen 18-time grand-slam champion Federer now holds a 20-3 head-to-head record against his compatriot, who did not do a lot wrong but was simply unable to stop the rampant ninth seed - who will move up to sixth in the world on Monday.
Wawrinka, seeded three, became the only player to break Federer this week in a high quality showdown which lived up to expectations.
An expectant crowd were treated to an exhibition of serving from both players right from the start, while also showing some delightful touches as seen so many times down the years.
It was not until the 10th game that the first break point came and Federer grasped his chance, winning an epic rally when Wawrinka - who opted not to challenge when he appeared to serve an ace earlier in the game - sent a forehand long.
Wawrinka showed an excellent reaction to falling behind, quickly putting Federer on the ropes at 0-40 in the first game of the second set and duly breaking his compatriot.
He was unable to keep the upper hand, though, as a purring Federer, playing his seventh final at Indian Wells, levelled at 2-2 with a rasping forehand winner after Wawrinka was put on the back foot.
Neither player could force another break point until Wawrinka netted to give Federer match point, which he won with a volley to spark more celebrations.