"I have totally exceeded my expectations. My goal was to be top eight by Wimbledon. This is just a dream start," Federer, who will climb four spots to world number six on Monday, said courtside.
"I understand the talk about (me getting back to) world number one with Andy (Murray) and Novak (Djokovic) not playing well and I'll try to back it up. But this is my 90th (tour-level) title so I'll try to enjoy this first."
He was granted a bye in the quarter-finals when Nick Kyrgios, who beat Novak Djokovic, withdrew with illness but he beat Jack Sock in the semi-finals to set up the clash with Wawrinka.
Roger Federer à Indian Wells.
Image credit: AFP
Both players produced some crowd-pleasing shots but Federer took the opening set 6-4.
Wawrinka battled hard in the second, breaking in the opening game, but in the end he couldn't compete with Federer who powered to his fifth win at Indian Wells.
"I was very sad when I couldn’t come here last year so just being here is a beautiful feeling," Federer said during the trophy presentation.
"It's been just a fairytale week. I'm still on the comeback. I hope my body is going to allow me to keep on playing.
"I came here for the first time 17 years ago so to be here again as the champion is an amazing feeling. And I can’t tell you enough what it means to me."