City face a tough test to rescue their Champions League hopes following the last 16 first leg defeat to Barca, who took the lead at the Etihad Stadium through a Lionel Messi penalty following a foul by Martin Demichelis.
Demichelis was sent off for his challenge, but replays suggested the tackle had taken place outside the box.
Dani Alves compounded City's misery with a late second and Pellegrini was uncharacteristically outspoken about the performance of Swedish referee Jonas Eriksson afterwards.
Pellegrini asserted that UEFA should not have selected a Swedish official for the match, statements that are now being investigated by European football's governing body.
However, the Chilean has now backtracked on those remarks, insisting that he did not intend to insult the Scandinavian nation.
"When you lose a game the way we lost against Barcelona, you are frustrated, you are angry," Pellegrini said.
"Maybe I say some things I didn't mean in that way so I apologise for what I said.
"Also I want to clarify what I said, I didn't make any serious accusations to anyone, not to the referee, not to UEFA, not to anyone.
"I say the referee decided the match because he decided the match because he didn't give us a foul against (Jesus) Navas and after came the penalty against Martin Demichelis and we had one player sent off.
"The referee decided the game. A lot of time he didn't give the foul. It's a difficult profession, he had a bad day and I didn't say that he was a bad referee.
"The second thing that is also not the way I think is to say because he was always refereeing in the Swedish league that maybe it was better for so important a game to have another kind of referee, it is another thing I didn't think.
"It is not an offence to Sweden or the Swedish people or referees. Sweden is a country that has a lot of good players, they have one of the best in the world in Zlatan Ibrahimovic and it can also have a good referee."
