"That defeat was a dagger through the Bavarian heart," admitted Bayern chairman Karl-Heinz Rummenigge after the holders progressed thanks to the away-goal rule as the Last 16 tie ended in a 3-3 draw on aggregate.
"We’re deeply, deeply disappointed.
"We weren’t the worse team. We deserved to go through, but unfortunately, football can be brutal at times."
After Inter - then coached by Jose Mourinho - also beat Bayern 2-0 in last season's Champions League final this was another bitter pill for the Germans to swallow.
Goals by Bayern's Mario Gomez and Thomas Mueller were cancelled out by Inter's Samuel Eto'o and Wesley Sneijder before Goran Pandev scored the Italians' crucial third in the 88th minute.
It was hard to take for Bayern, who at one stage led 3-1 on aggregate and squandered at least two clear chances, leaving Rummenigge smarting.
"It was all looking good at half-time," he said.
"In the first half, I saw a great game of football and a magnificent Bayern team.
"But if we’re to be accused of anything, it’s our failure to protect a 2-1 lead until the end. We were a little too naive."
Despite being told by Rummenigge his contract will be terminated at the end of the season -- a year earlier than planned -- Bayern coach Louis van Gaal now has to lift the players before Saturday's league game at Freiburg.
After their Champions League exit, having been knocked out of the German Cup and effectively out of the Bundesliga title race, Bayern will finish the season without silverware.
They need to finish second in the German league to be sure of a Champions League place next season and are seven points off the pace with eight games left.
Despite leaving at the end of the season, Van Gaal has said he will not walk out early.
"The coaching staff and I will now concentrate on leading the team out of this trough," the Dutchman said.
While the hunt for a new coach goes on, Rummenigge says the players will need to show their professionalism.
"A game like that is bound to leave scars, but there’s no point crying about it," he said.
"We have to pick ourselves up for Saturday to salvage what can be salvaged in the Bundesliga.
"I hope we can still achieve what we need: qualification for the Champions League."