The 21-year-old Wales international -- who signed from second tier Swansea in the close season -- sealed victory after David de Gea had saved a spot kick from Daniel Maldini, son of legend Milan and Italy Paolo.
United's 5-4 victory -- their other five victories have included beating Tottenham Hotspur and Inter Milan -- in the shootout came after the match ended 2-2 but was not enough for them to win the International Champions Cup with the honours going to Portuguese side Benfica instead.
The English side's triumph came despite the absences of Belgium striker Romelu Lukaku, who is expected to leave the club with a potential swap deal with Argentinian Paulo Dybala from Juventus in the pipeline, and France's World Cup winning midfielder Paul Pogba.
Pogba purportedly missed the trip to Wales with a back injury although the Daily Mirror on Saturday claimed he had sought to seal a move away by not travelling with the squad.
United took the lead when Marcus Rashford opened the scoring with a delightful individual effort, dancing through two rather feeble efforts at tackles before his shot took a deflection off Milan skipper Alessio Romagnoli.
The visitors levelled in the 25th minute, Suso -- who had gone close minutes before -- scoring a lovely goal curling it into the net from outside the penalty area.
De Gea denied Suso, who had an unsuccessful three year spell at Liverpool from 2012-15, a second seven minutes before the break as he reacted brilliantly to deny the Spanish international midfielder.
De Gea also had to be alert to prevent Milan going ahead a few minutes later getting a hand to Krzysztof Piatek's lob.
Suso was at the heart of the goal that gave Milan the lead on the hour mark, his cross being flicked on by Samu Castillejo which hit United central defender Victor Lindelof's head and went into the net.
United struck back, though, to level as substitute Jesse Lingard's shot beat former Liverpool goalkeeper Pepe Reina with 18 minutes remaining.