Murray looked disinterested at times as the switched-on Swiss blew him away with accurate serving and dominant ground-strokes, the British number one not helping himself with some terrible unforced errors.
Wawrinka will now face Jo-Wilfried Tsonga in the quarter-finals, while Roger Federer returns to the world number two slot despite not lifting a racquet.
After a bright start to the match in which he earned two break points at the first time of asking, Murray collapsed to lose the next six games – including three breaks – as the Swiss exploited some lazy, disinterested play from the British number one with a contrasting display of power and precision.
Murray appeared to snap out of his malaise in the second set, even saving a break point with three brilliant shots under pressure.
But Wawrinka was not letting up, dominant at the baseline as he happily switched from backhand to forehand, while Murray appeared to lose interest again as he was broken following a terrible missed volley with the Swiss stranded.
The Scot was broken again at the last, yet another unforced error doing for him as he served to stay in the match, and he was booed by the French fans while ambling off court.
"I made a lot of mistakes - 24 unforced errors is far too many, that's where half the points went," Murray told a news conference. "I started hitting the ball shorter, then he was able to dictate the play."
Wawrinka said Murray's negative body language is easier to read when he plays badly on clay.
"I think when he's not feeling that good, he cannot just play from the baseline against me. For me it's perfect because he's playing so slow," Wawrinka said. "
You never expect to beat a top-four player, especially that easy."