Undermanned Bayern, nursing a bulging casualty ward, set the tone in the first half-hour, with Michael Olise and Harry Kane narrowly failing to break through. Inter opened the scoring on the 38-minute mark when Marcus Thuram's clever back-heel found Lautaro Martinez, who blasted home.
The Italians maintained control until Bayern veteran Thomas Mueller, days after announcing a summer departure after 25 years at the club, scored the equaliser with a typical poacher's finish with five minutes remaining.
Not content to be spectators to a Bayern fairytale ending, Inter broke on the counter just three minutes later, with Frattesi who scored Inter's second.
Inter, defeated in the final by Manchester City two seasons ago, have their noses in front in their bid to make the last four of the competition. The late goal consigned Bayern to their first home defeat in the UCL since 2021, a run of 22 matches.