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There was a scare for the German champions when Franck Ribery limped off towards the end of the first half, but coach Carlo Ancelotti said later he suffered a minor ankle injury and would be back in action in days.
Bayern dominated early on but it was Inter that managed to get a goal in the eighth minute against the run of play.
An Antonio Candreva cross found 30-year-old Eder, who dispatched his header past the Bayern goalkeeper Sven Ulreich.
Playing in front of a crowd of about 23,000 in the city-state’s main stadium, Inter scored their second in the 30th minute on another quick counter attack.
Croatian winger Ivan Perisic picked out Eder with a pin-point cross, leaving the striker to score his second header of the game.
Ribery had seemed the biggest threat for Inter, although the German champions seemed to lack their usual cutting edge.
But four minutes after the second goal, he left the pitch with an injury, with the Frenchman substituted for Milos Pantovic.
Bayern said Ribery needed stitches for a cut to an ankle but Ancelotti added it was a “small problem” and the player would be back in action in three to four days.
Eder did not get the chance to complete a hat-trick as he was taken off on 50 minutes by Inter coach Luciano Spalletti for Gabriel Barbosa.
Bayern grew into the game but never looked completely comfortable, even with the introduction of Thomas Mueller, who scored two goals in the side’s 3-2 victory over Chelsea in a friendly match in Singapore Tuesday.
The result was a boost for Inter Milan boss Luciano Spalletti, who took over at the club last month.
“Overall, Inter played a very good game,” he said after the match.
“I’m very proud of my team. We played very well on the defence line as well as the forward line.”
Despite the disappointing result, Bayern boss Carlo Ancelotti praised the performance of Renato Sanches, who came on as a second-half substitute.
The Portuguese midfielder had a disappointing first season at Bayern and AC Milan and Manchester United are rumoured to be chasing him.
“I’m really happy for him because he had this quality also last year but he was not able for some reason to show this, now he is showing this and he is an important player for us,” said Ancelotti.
The game was part of the International Champions Cup, which brings together top-tier teams from Europe.
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