Pellegrini said Swedish official Jonas Eriksson "favoured Barcelona from the beginning to the end" after he sent off Martin Demichelis and awarded Barca a penalty, despite arguments that the decisive contact was made outside the area.
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"He's right," he told reporters. "The referee was not up to a decisive game. The Demichelis foul on Messi was outside the box and changed everything."
The Montengro international, who moved from Fiorentina for around £22 million last summer, did not feature against the Catalans.
And while he admitted that he was disappointed not to play a part, and says Florence is "clearly more beautiful than Manchester", he insists he is happy to fight for his place at the Etihad Stadium.
"It happens, the coach makes choices and I have to respect them," he added. "I was fine, I wanted to play at least a little because these are the nights that every player dreams of experiencing. But I have to be patient."
After being prompted that he could have played in the absence of Sergio Aguero, he replied; "Exactly. Do not make me say more, try to understand. City are one of the best teams in the world, the competition is high."
Goal reported in December that a number of Serie A clubs had enquired about a transfer during Jovetic's injury lay-off, and there were further reports in Italy about an approach from Roma and Juventus, but he says he was never interested in leaving.
"I read it too, of course," he continued. "But there was nothing. I would never come back [to Italy] after only six months. I feel good here.
"I had always played before my injury. I admire Pellegrini, I know him, I wanted to play for him. Now I have to try to catch up. But back to the question: no, I have not regretted the move.
"I miss Florence a lot. I miss the city, which is certainly more beautiful than Manchester, and I miss my friends. But do not misunderstand me, otherwise the headlines will say: I'm thinking of going back to Fiorentina.
"It's hard to predict but I signed a long contract with City and I intend to honour it. I want to prove myself in such a competitive group."