Barca, who lifted the trophy in 2009 and 2011, were the favourites to win the competition ahead of Tuesday's semi-final first leg but they were so outclassed by the Germans that many pundits believe their recent spell of dominance is over.
"I think it is unfair to talk of a cyclical change," the Spanish World Cup winner said.
"Over the last five years this team has won two Champions League titles...and we are on the point of winning a fourth La Liga title.
"It makes no sense to analyse five years in the one match in Munich. For me the end of an era is when years go by and you don't win any titles."
Barca, 13 points clear with six games left, will be crowned La Liga champions again on Saturday if they win at Athletic Bilbao and second-placed Real Madrid lose the city derby at Atletico.
"When you win the league you cannot say it has been a bad year because it is the most important title," said midfielder Iniesta.
With Real also suffering a heavy 4-1 defeat at Borussia Dortmund in their Champions League semi-final first leg, Iniesta was asked if the Bundesliga had overtaken La Liga in importance.
"Bayern and Borussia are very good teams, well prepared physically and technically, and they have shown it in these two games," Iniesta said.
"It isn't that La Liga has dropped below them, it is just that the teams have overcome their rivals."
Looking ahead to Wednesday's second leg at the Nou Camp, the 28-year-old promised Barca would give their all in a bid to turn the Champions League tie round.
"We have 90 minutes in front of us to try and achieve something very difficult," Iniesta said.
"I can't sit here now and say we will score five goals against Bayern but the team will head out with that mentality."
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