Barca captain Messi nonchalantly opened the scoring with a 'Panenka' penalty chipped down the middle of the goal in the 17th minute after Luis Suarez was fouled in the area, putting his side ahead in the tie after a goalless first leg in France.
Suarez then rounded Lyon goalkeeper Anthony Lopes to lay on a perfect pass for the unmarked Philippe Coutinho to nudge into an open net and double Barca's lead, although Lyon hauled themselves back into contention with a second-half strike from Lucas Tousart.
Messi soon killed off any hopes of an unlikely comeback from the French side, however, carving his way through the defence to score in the 78th minute before toying with Lyon's back line twice more and laying off passes for Gerard Pique and then Ousmane Dembele to complete the rout.