Manchester City boss Manuel Pellegrini said Swedish referee Jonas Eriksson favoured Barcelona in the Spanish side's 2-0 victory at Etihad Stadium.
Eriksson awarded Barcelona a penalty and sent off City defender Martin Demichelis as the visitors won the Champions League last-16 first-leg tie.
Pellegrini claimed Eriksson was "not impartial to both teams".
The Chilean added: "The referee decided the game. He was on Barcelona's side from the beginning until the end."
Uefa will await reports from the referee and match delegate before deciding whether to charge Pellegrini with misconduct for his comments.
Demichelis was sent off for a 54th-minute foul on Lionel Messi, who converted the resultant penalty to break the deadlock.
Pellegrini said a referee from Sweden that "doesn't have enough experience" should not have been chosen to officiate the game, and claimed Eriksson had "arranged" a mistake he made in Barcelona's Champions League quarter-final against AC Milan in 2012 when he failed to award a penalty despite strong appeals.
Pellegrini added: "Before the penalty, which was outside the area, there was a foul on Jesus Navas. He didn't control any of the game.
"I think it was not a good idea to put a referee from Sweden in charge of such an important match, and a referee who made an important mistake against Barcelona in a previous match. Today he arranged it.
"The more important mistake is the foul against Navas, and secondly the penalty.
"Contact was outside the box - that is the foul, you cannot continue the foul. The first foul is outside the box. Before the penalty Barcelona did not have chances and we were preparing the way to score."
Pellegrini spoke to Eriksson at the final whistle and said: "I just told him he decided the game and he must be very happy because he decided the game."
The normally taciturn Chilean added: "I think there is more important football in Europe than Sweden. This is a big game with two important teams and maybe in this type of game you need a referee with more experience."
City captain Vincent Kompany insisted his side could still win the tie, despite Barcelona doubling their lead just before full-time through Dani Alves.
"If the game is the same as today, and we manage to stay away from some fouls, we have got a chance [in the second leg]," he told ITV Sport.
"There was a lot of soft fouls. In the Premier League they would have not been given."
The return leg takes place in the Nou Camp on Wednesday, 12 March.