Premier League champions were 2-0 down and being outplayed in Spain before Jamie Vardy scored what could be a crucial away goal 17 minutes from time.
Bonucci was punished by Allegri for an argument towards the end of the win over Palermo last Friday.
Arsene Wenger's side have won once and lost four times against other clubs currently in the Premier League's top seven.
Kasper Schmeichel gave Leicester City a lifeline despite his team losing 2-1 in the first leg of their Champions League tie away to Sevilla.
Bayer's claims to being Germany's third-best team are under threat. Tuesday's loss to Atletico signalled what could be the start of a very big slide.
Even playing a man up, Massimo Allegri says Porto threatened all match, and Juve had to bide their time to score.