Wawrinka and Tsitsipas were playing in one of matches of the tournament on Court Suzanne Lenglen while Federer cruised through against Leonardo Mayer.
On match point, the two played out another lengthy rally and Tsitsipas looked to be in control when he hit an inside out forehand and attacked the net.
From well wide of the tramlines, Wawrinka sliced a backhand just over the net and beyond the Tsitsipas, who thought the ball was out.
But the umpire came down from their chair, looked at the line and deemed the ball to have caught the outside of the line.
FRENCH OPEN RESULTS: LATEST RESULTS FROM THE MEN’S DRAW
And Wawrinka will now face his fellow Swiss Federer in the last eight on Tuesday.
Speaking in an interview with Eurosport, Federer was asked for his take on Wawrinka’s battle with Tsitsipas and said: “That was unbelievable. I saw some of it, I was in the press conference.
“I think I was also playing at the same time. And I watched pretty much the fifth set, that was unbelievable.
“It had everything, the crowds loved it. They probably would have liked a little more too. But Stan was happy it ended.”
Federer then saw footage of the match point and said: “That was a sick pass at the end on match point. Jesus, right on the line.
“Stan did amazing, I was really happy for him. Especially since his knee problems which were severe.
“They were tough so it is nice to see him back to winning ways.”
Federer later revealed he intends to rewatch his defeat to Wawrinka in 2015 to see what he can do better.
“It’s different times. He was on a roll at the time, obviously he’s on a roll at the time, and he is now but it’s a different year,” he said.
“We’ve both had knee surgeries in the meantime. I don’t know – a lot has happened since. I’d say in that match it was a little bit windy.
“It was a good day then I believe, sunny. It was Lenglen then but is it going to be Chatrier tomorrow – we’ll see? Is it going to be raining? Is there going to be wind? All of that will play into the occasion. Is Stan going to be tired or not? I don’t know.
“So a different game. I will look back at that match [in 2015] and see what did I do right and wrong? And same, what did he do so well, but I know that when Stan gets rolling he can crush the ball from back and he’s just very hard to stop on clay.
“That’s why sometimes the match in his racket and that’s why he’s tough to play.”
Watch every minute and match from Roland-Garros 2019 live – anytime and anywhere – on Eurosport and the Eurosport Player.