Barcelona advanced with a 4-1 victory on aggregate over two legs in which referees decisions and non-decisions played a big part.
City defender, Joleon Lescott, was unlucky as Cesc Fabregas’ pass bobbled through his legs in the 67th minute to emerge onto the run of Messi, who flicked the ball over goalkeeper Joe Hart.
As in its 2-0 defeat in the first leg, City finished with 10 players after Pablo Zabaleta was booked for a second time in the 78th minute for protesting after Gerard Pique barged into substitute Edin Dzeko inside the area without a penalty being awarded.
Vincent Kompany scored a consolation goal for City in the 89th minute before Dani Alves struck in stoppage time for the Spanish champions.
In the night’s other match, Paris Saint-Germain advanced to the quarterfinals for the second straight season after coming from behind for a 2-1 win over Bayern Leverkusen and a 6-1 victory on aggregate.
Pellegrini watched from the stands as the Chilean served a ban for his criticism of the referee’s performance in the first match.