The euphoria inside a packed Nou Camp was tempered, however, when Lyon scored either side of halftime through Jean Makoun and Juninho to give themselves a ray of hope.
But their chances of progressing had all but disappeared by the time substitute Seydou Keita went clear in added time to score past Hugo Lloris and round off a superb Barca performance.
Coach Pep Guardiola said it had been one of the best of the season. "We had a little fright when they scored their second but we managed to plug the gaps," he said at a news conference.
The Catalans showed few ill-effects from a recent poor run of form and dominated the opening stages. Midfielders Xavi and Andres Iniesta orchestrated some trademark, slick passing moves and both Eto'o and Iniesta had good early chances.
Lyon had to wait for almost 20 minutes for their first scoring opportunity when Karim Benzema broke clear on the left but Ederson was unable to convert the striker's low cross.
ROCKED BACK
Barca's breakthrough came in the 25th minute when Rafael Marquez chipped a pass to send Henry clear down the middle and the France international, scorer of the goal in the 1-1 draw in the first leg, finished with ease.
Xavi was the provider for Henry's second two minutes later, releasing him on the left of the penalty area to send a powerful shot inside the bottom corner.
Messi's goal on 40 minutes was typical of the Argentine international. After cutting in from the right and leaving several Lyon players in his wake he exchanged passes with Eto'o and slotted calmly past Lloris.
Henry turned provider three minutes later when he released Eto'o in the centre and the Cameroon international powered the ball into the top right corner to make it 5-1 on aggregate.
Barca were temporarily rocked back when Makoun rose to nod in Juninho's corner on 44 minutes and Benzema cleverly let Cesar Delgado's cross run on for Juninho to make it 4-2 on the night just after the break.
Juninho was shown a second yellow card in added time after having words with Brazilian compatriot Daniel Alves lying prone on the ground after a clash with Fabio Grosso and Keita's goal five minutes into stoppage time was the final action of a high-quality match.
Lyon coach Claude Puel paid tribute to Barca's ability to maintain possession and starve his side of room.
"I think you just have to praise this Barcelona team," he told a news conference. "They showed they were superior tonight in all areas and we just have to accept that."
