Fourth seed Federer turned on the style to demonstrate that he is more than capable of claiming an eighth title at the All England Club in a 3-6 7-6 (7-5) 6-4 6-4 victory on Court Number One.
Wawrinka described facing Federer at Wimbledon as "one of the biggest challenges in tennis" ahead of their last-eight showdown and the Australian Open champion was unable to overcome his compatriot after a promising start.
Federer crashed out in the second round with a shock defeat to Ukrainian Sergiy Stakhovsky last year, but the 17-time grand slam champion has looked a force 12 months on and will now face either Milos Raonic or Nick Kyrgios at the semi-final stage.
World number four Wawrinka had never previously progressed beyond the fourth round at Wimbledon and fatigue appeared to get the better of him as he crashed out in the last eight.
Federer had not dropped a set on his way to the quarter-finals, but Wawrinka ended that record as he took the upper hand by securing the solitary break in the opener.
A forehand volley from Wawrinka did the trick as he took the third opportunity to break in the fourth game in order to take a 3-1 lead and Federer found himself a set behind as his countryman went a set up courtesy of a forehand winner.
Fifth seed Wawrinka fashioned the only two break points of the second set, but Federer stood firm and edged a tie-break to level the match and Wawrinka called for the tournament doctor at the end of the set but opted not to use a time-out.
Federer had the bit between his teeth and the game swung in his favour when he capitalised on a loose forehand and then an unforced error on the Wawrinka backhand to take a 4-3 lead.
He needed just one set point to move within a set of a last-four berth and produced a smashed forehand winner to do just that.
Federer had a spring in his step, while Wawrinka appeared jaded in the final set and there was no stopping the 32-year-old as he avoided a five-set endurance test.
A break in the third game did the trick and, although Federer made hard work of getting over the line as he needed five match points to finish off the job, he was able to celebrate moving a step closer to another final.