The 22-year-old, on at half-time, saved twice from former Liverpool players Fabio Borini and Suso as United won 9-8 on penalties in a shoot-out that lasted 13 rounds with all 11 players taking at least one.
Pereira had the chance to win it at 3-2 but saw his spot-kick saved by Pepe Reina. Chris Smalling had initially stepped up to take the decisive kick but was called back by Jose Mourinho in favour of Pereira. Smalling scored in the next round.
It was a repeat of the shoot-out between the same two teams in New York in 2004, with Milan running out 9-8 winners.
United started well and AC Milan goalkeeper Gianluigi Donnarumma was forced to save a Scott McTominay shot from the edge of the box and an Alexis Sanchez free-kick inside the first 10 minutes.
It no surprise Sanchez got the opening goal after 11 minutes -- United's first from opening play on this tour -- after latching on to a delicate lob over the Milan defence from Juan Mata.
The lead lasted just four minutes with Suso taking advantage of some sloppy defending from Chris Smalling, Eric Bailly and Axel Tuanzebe -- starting as a back three -- which allowed a long ball from Leonardo Bonucci to skid through.
Ander Herrera might have put United back in front before half-time but saw his shot saved by Donnarumma after quick break involving Luke Shaw and Sanchez.
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