The Manchester United star started on the bench after a series of poor displays.
But with the Red Devils level with their opponents Mourinho turned to the World Cup winner.
Fans were quick to disapprove though as they booed the introduction of Pogba.
The central midfielder has struggled to impress this season as United sit way down in eighth in the Premier League.
And fans couldn’t believe what they were hearing on social media.
He tweeted: “Did some of our own fans just boo Pogba. I’m finished.”
Another added: “Pogba boo’d as he came on from the home fans. The club is falling apart, Well Done Jose.”
And a third explained: “Boos when pogba comes on. Jose really is deceiving the fans. Astonishing.”
The game ended 2-2 after a back and forth battle at Old Trafford.
An error from David De Gea helped Shkodran Mustafi’s header into the net before Anthony Martial replied quickly.
The match exploded in the second half with a Marcos Rojo own goal giving the lead back to Arsenal.
But Jesse Lingard netted seconds later to equalise.
United now sit eighth in the Premier League, eight points behind Arsenal.
And Mourinho’s side are a massive 18 points behing champions Manchester City.
United return to action against Fulham at Old Trafford in the Premier League on Saturday (3pm).