Published: 2019-03-14 04:04:50 BdST
Barca captain Messi opened the scoring with a "Panenka" penalty chipped straight down the middle in the 17th minute after Luis Suarez was fouled in the area, putting the home 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.
Barca coach Ernesto Valverde had warned his side of complacency after Paris St Germain and Real Madrid's surprise exits, and his words carried more weight after Atletico Madrid were knocked out by Juventus despite a 2-0 first leg win.
His side were in a more vulnerable position as a score draw would have sent them out, and they began the game as if they meant business, with Messi firing an early shot which Lopes had to beat away for a corner.
Lyon's Lopes had to be taken off injured later in the first half, leaving the field in tears after taking a blow to the face, with Mathieu Gorgelin replacing him and making his Champions League debut.
Barca looked unsettled for a brief period after Tousart's goal had put Lyon one goal away from knocking the Catalans out, and the home side defended with an air of panic.