However, Murray, described as the real no 1 by fourth round opponent Juan Del Potro, bounced back by taking the second set easily and stormed through a third-set tie-break before finishing off a tiring Nishikori to seal a fourth successive semi-final appearance in Paris.
The 2015 champion demolished Marin Cilic, who has been in fine form himself this fortnight, 6-3 6-3 6-1 in just 100 minutes.
Murray's clash with Wawrinka is a repeat of the 2016 semi-final in Paris, which the Brit won in four sets.
"Stan has played fantastic this tournament so far", said the Scot, who was beaten by Novak Djokovic in last year's showpiece.
Murray said the incident had not had a major impact on the match but it certainly got him going, having been outplayed in the early stages as Nishikori, who beat him at the same stage of the US Open, took his groundstrokes early and rushed Murray into mistakes.
"It's not always been easy for me here".
Spain's nine-time champion Rafael Nadal will play Austrian eighth seed Dominic Thiem in the second semi-final. Hard question. So far when I have beaten a top guy, I have always played a way worse match the following day.
Thiem knows he has a huge task to try to dethrone the king of clay but after a win over the Spaniard on the surface at the Rome Masters. He won in Geneva so is obviously confident.
Serving at 1-1, deuce in the second set Murray was bizarrely given a time violation warning by umpire Carlos Ramos after he had let an errant ball toss land - prompting an exchange of views between the pair.
"I played well, was very solid and took my opportunities". It's great. I'm really happy to be in the semifinal here.' About his next match against Andy Murray, Wawrinka said: 'It's going to be interesting match, for sure.
Murray dropped the opening game of the fourth set on his serve and then swept Nishikori aside, beating the Japanese player for the ninth time in 11 career meetings. "I think physically and mentally I feel ready", he said. I think he's probably a bit less confident, a bit more hesitant.
"It was ideal today, I'm very satisfied", said Wawrinka who will be playing in his third successive Roland Garros semi-final.
Lendl told Press Association Sport: "Obviously winning is better but I knew the reasons why he is struggling. It felt to me like it was a odd decision", he said. Sometimes, you just have to do what you have to do to win the match.
Meanwhile, Simona Halep staged a remarkable fightback and saved a match point to reach the semi-final with a 3-6 7-6 (6) 6-0 win over Elina Svitolina yesterday. Kei missed a second-serve return, and then I think a good serve on the next point. All four players are seeking a first grand slam title.