The 20-time Grand Slam champion booked his place in the semi-finals with a 6-7, 7-6, 6-2 win over his Swiss compatriot at the Lindner Family Tennis Center in the early hours of Saturday morning UK time.
Wawrinka is only just back from a long-term knee injury which has seen him sink down the rankings to world No 151 but he claimed the first set in impressive fashion.
Yet while he was just two points away from taking the second set and making the final four, World No 2 Federer – a seven-time winner at this tournament – bounced back on the hard court.
And the first seed benefitted from a later break due to adverse weather conditions, breaking for the first time at the eighth attempt, to eventually come out on top at the Masters 1000 tournament.
Yet despite claiming the spoils, Federer revealed his delight at seeing his friend Wawrinka back in better shape after their two-hour, 16-minute clash.
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“Stan has the power, and I’m so glad he’s back on the tour and playing well and moving well. So I really enjoyed the match for what it was,” Federer told ATP World Tour.
“It’s difficult to always play against him, but I’m happy I was able to find a way in the breaker in the second, because it was a frustrating night, for me, for the most period, and in the third I was able to find a way.
“I think it was partially because he maybe dropped his level, for sure, but maybe me, I also played a bit better then.”
Federer was in action twice in one day, beating Leonardo Mayer in straights sets in a third round match delayed by rain before later returning to see off Wawrinka and move an eighth Cincinnati semi-final.
And his countryman also had to complete a double-header, beating Marton Fucsovics before returning to court later the same day.
Federer added: “It was exciting to go through something new, only it was something I have done for the second time of my career maybe at the professional level.
“Felt like two separate days, actually, because this morning it was daytime, or this afternoon it was daytime, windy and breezy.
“And then we came out in the nighttime and it was black, and the sky [was] totally different. No wind at all. Different atmosphere. It was quite interesting, actually,”
Wawrinka said: “For sure it was a great level. I think I’m playing great in general. I’m playing better every day, every week.
“Last week was really important and really good for myself, for my tennis, for my confidence. I’m happy to see where I am right now. I had a tough match last week against Rafa [Nadal]. Close match, also.
“Today was against Roger. They are No. 1 and No. 2 in the world. I beat [Diego] Schwartzman, I beat [Kei] Nishikori, so the level is good.
“I need to keep improving, keep working, keep doing the right thing and keep pushing myself. For sure tonight I’m sad and disappointed to lose, but for me it’s a big victory for myself after what I had last year.
“It was exactly one year ago. To see where I was also few weeks ago, I’m really happy to be here.”
Federer faces Belgium’s David Goffin in the semis after Novak Djokovic takes on Marin Cilic in the other final-four match.