That goal sealed Barcelona's place in the semifinals for the sixth consecutive year and defender Gerard Pique believes his side ran out worthy winners.
"I think Barca has shown a lot of quality in the six years and I think we deserve it again to be in the semifinals," Pique told Sky Sports.
"Paris St-Germain is very strong with good quality but I think we deserved it.
"In the first leg we deserved a little more and tonight we're very happy to have qualified.
"It doesn't matter if he's a little bit injured he can change everything.
"We are very proud and lucky to have him in our side. He's our reference as a striker - he can score, he can pass he can do anything and everything."
PSG coach Carlo Ancelotti added: "I thought we played well. We caused Barca problems, but Messi is a fantastic player and can find a solution for his team even when not fully fit."
In the night's other game, Bayern Munich produced a hugely impressive performance to book its place in the last four courtesy of a 2-0 win over Juventus.
Leading 2-0 from the first leg, Bayern eased past the Italian side thanks to goals from Mario Mandzukic and Claudio Pizarro.
Bayern, which lost in the final to Chelsea in Munich last year, joins Bundesliga rival Borussia Dortmund in the semifinals.
It is the first time two German clubs have made the last four of the competition in the same season.
And winger Arjen Robben, who was denied a goal of his own by the woodwork, is keen to avoid Jurgen Klopp's side in the next round.
"If you win away 2-0 in Turin here I think that's an amazing result because they are unbeaten for I don't know how many games and they are so strong at the back," Robben told Sky Sports.
"Even more, if you dominate the game in the second half as we did, it is a great performance.
"We would like to be kept apart from Borussia Dortmund in the semifinals but we don't have a choice and it comes out how it comes.
"It going to be a big one and the semifinals have maybe the four best teams at the moment."
Bayern will now compete in their third semifinal in four years, but it must do without Mandzukic in the first leg with the Croatia star set to serve a one-game ban.
Juventus goalkeeper Gianluigi Buffon believes Bayern's extra experience was a key factor in the outcome of the tie.
He told Sky Sports: "The big difference between them and us is experience. I was even more impressed tonight than in Munich.
"In the first leg we did not give our all, but tonight we did and still there was nothing we could do. I think Bayern can win the Champions League."