Messi and Dani Alves had given Barca a 2-0 first-leg advantage at the Etihad Stadium and the same duo were on target again in a 2-1 win over the Premier League side at Camp Nou in the last 16 return clash on Wednesday.
The Catalan giants have lost three of their last six La Liga games to slip to third in the table domestically, but they are still in the hunt for the treble after securing their place in the quarter-finals of Europe's premier club competition.
Vincent Kompany had equalised a minute from time for City after Pablo Zabaleta was sent off for showing dissent following referee Stephane Lannoy's failure to award a penalty.
Alves then scored a stoppage-time winner and the Spanish champions could have won by a more emphatic margin if Messi had been awarded a first-half spot-kick when he appeared to be fouled by Joleon Lescott, before Neymar had a goal wrongly ruled out for offside.
The Argentina forward now has 28 goals for the season and he was left to reflect on a job well done as Barca eased the pressure on coach Gerardo Martino.
"We knew we had to get a goal to calm ourselves down because of the potential they have," Messi said.
"In spite of their goal, I think that the tie was never in danger. We played well throughout and achieved our objective of getting through.
"After two very serious slip-ups in the league, in games where we didn't play well, today we saw the Barcelona that people expect to see and we defeated a very difficult rival."
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