The Japan international had just created the Reds’ second equaliser with a shot that hit both posts and fell to Robin van Persie, when he was replaced by Javier Hernandez.
A few minutes earlier, Ryan Giggs had been brought on in place of Wayne Rooney and Sir Alex admitted he should probably have left Shinji on as the Premier League leaders hunted a winner.
The United manager said: “As far as taking Rooney off the other night, it was simple: he wasn’t playing as well as Shinji was. In so many games Wayne is better than most players but on the night Shinji was playing so well.
“The ironic thing was, when we were chasing a goal with 14 minutes left, I decided to put Chicharito on and Shinji made the second goal.
“I’d already given the fourth official the card, Chicha was standing on the touchline and then we scored the second goal. I think if I’d have changed my decision then we would have won it.
“Shinji was doing really well but unfortunately he came off. Chicha came on simply because you always think he’ll get a chance in the game. At that point we wanted to win it and you make decisions like that that maybe are not fair.”
Shinji has impressed in recent games, playing either on the left or just behind a striker, and also made United’s first goal at Upton Park for Antonio Valencia after a neat one-two with van Persie opened the Hammers up.