Mario Gomez looked marginally offside when he turned in Thomas Mueller's header from close range for the second goal in the 49th minute.
The two-goal Mueller also appeared to obstruct Jordi Alba when the full-back attempted to stop Arjen Robben as the Dutch international winger ran through to score Bayern's third after 73 minutes.
"I don't want to talk about the referee but it's clear they scored two illegitimate goals," Roura said.
"In every game we have played away from home, against AC Milan and Paris St Germain, there have been debatable decisions but I don't want this to be an excuse.
"There were illegal goals but we mustn't take away credit from our opponents. Bayern were the better team and we were not able to resist their physical pressure."
Bayern coach Jupp Heynckes said he did not have a perfect sight of the two disputed goals from the bench.
"When you're on the touchline it's very difficult to have a clear view of what happened," he explained.
Champions League matches feature five officials, including one on each goalline, to spot infringements in the penalty area.
UEFA say the system is more efficient than employing goalline technology.
Heynckes is not taking Bayern's place in the final at Wembley in May for granted despite the one-sided scoreline on Tuesday.
"I am happy about the result but I am not moved by it. I know we still face 90 very difficult minutes in Spain," he said, referring to the return game at the Nou Camp on May 1.
"We will enjoy what happened tonight but no more. It is important to stick to your tactical guidelines against Barcelona and that is what makes my team stand out this year.
"We have been displaying extraordinary football for the entire season," said Heynckes of a Bayern squad that have already been crowned Bundesliga champions and are also through to the German Cup final against Stuttgart in June.
"Falling short of success in the past two years has only made them more hungry to win this year. The tactical awareness of this team is top notch as well, just like their willingness to run and fight for one another."