Juventus were almost perfect for the first hour as they led 2-0 in the round of 16 second leg tie and gave Pep Guardiola's Bayern a footballing lesson in their own Allianz arena. But two substitutions by Allegri handed the initiative to Bayern who hit back with two late goals to level at 2-2 and then scored twice more in extra-time to win 4-2 and 6-4 on aggregate after an extraordinary, see-saw tie.
First, Sami Khedira, who had been a rock in midfield, was replaced with the less experienced Stefano Sturaro.Almost immediately, Allegri took off forward Alvaro Morata, who had created Juve's second goal with a magnificent 60-metre run that left the Bayern midfield in his wake, and brought on Mario Mandzukic.
Until that moment, Juve's performance was a near replica of their previous visit to Germany, where they won 3-0 at Borussia Dortmund at the same stage of the competition last year.
Allegri set up an impenetrable barrier in defence, forcing Bayern to pass the ball sideways for most of the first hour, and picked off Bayern with level counterattacks. But they lost their attacking edge after the changes, with Mandzukic devoting most of his energy to provoking Bayern defenders and Sturaro looking uncomfortable in midfield.
In just 28 minutes after those changes, the Juventus defence, which has not conceded a goal in their last 10 Serie A matches, was breached four times to leave Italy without a team in the last eight.
One of the few moves they managed to string together after the changes broke down when Sturaro slipped and lost the ball.
Allegri admitted the course of the game had altered drastically, but omitted to say whether this was down to his substitutions.
"Nobody expected us to play like this against Bayern in Munich," he said. "We lost but we can be proud of our performance here. "We were leading 2-0 and had the chance to make it three. We played well and showed our qualities."
The coach was also let down by Juve's apparent lack of strength in depth.
Forward Paulo Dybala, midfielder Claudio Marchisio and defender Giorgio Chiellini were all injured and the remaining options, while perfectly adequate for Serie A, were not up to the task of challenging Europe's elite.
Allegri, however, has a habit of proving his critics wrong and is likely to bounce back. He was given a hostile reception by Juventus fans when he replaced Antonio Conte at the start of last season, but quickly proved them wrong by winning the Serie A and Coppa Italia and reaching the Champions League final.
Earlier this season, he was criticised for initially leaving Dybala on the bench.
Allegri insisted that the 22-year-old Argentine needed time, and has again been proved right as he has since gone on to score 14 goals and quickly turned into the most exciting player in Serie A.
(Corrects first Juventus substitution to Sami Khedira, not Juan Cuadrado fixes typo in 'in his wake', paragraph 5.)
(Writing by Brian Homewood; editing by Sudipto Ganguly)
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