A further one-game sanction has been suspended for two years.
Following the 2-0 defeat at the Etihad Stadium on February 18, during which Martin Demichelis was sent off, the Chilean claimed the Swedish official “decided the game”.
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"Of course I have a complaint, not only for the penalty and the red card,” said the City manager.
"I think in the whole match we didn't have a referee with impartiality to both teams.”
Pellegrini has since apologised for his comments but his sanction from Uefa means he will not be permitted to sit on the bench for City’s return leg against the Spanish champions on 12 March.
"You are frustrated and angry. Maybe I said something but I don't think that way. I want to apologise," said Pellegrini.
"I didn't say he was a bad referee, that he was not honest, that he cannot referee in Uefa.
"I felt from the beginning his criteria was not the same for both teams, I think he had a bad day - everyone can have a bad day - but I didn't say that intentionally he didn't give fouls for us or did give fouls for Barcelona."
The Chilean will not be allowed to communicate directly or indirectly with his players or coaching staff during the match at Camp Nou.