Pogba and Romelu Lukaku were named among the substitutes at Old Trafford following a disappointing draw away to Southampton at the weekend.
Pogba, in particular, was far from convincing at St Marys and Mourinho exploded at the Frenchman in the dressing room, labeling him a virus during a ferocious rant.
The midfielder was forced to watch on from the bench on Wednesday night as David De Gea uncharacteristically spilled Shkodran Mustafis header in the 26th minute to give Arsenal the lead. Anthony Martial hit back with an equaliser for United on the half hour mark.
A frantic second half ensued and Jesse Lingard rescued a point for the Red Devils immediately after Marcos Rojos 68th-minute own goal, prodding past Bernd Leno following some lackadaisical Arsenal defending.
Pogba replaced Lingard in the 75th minute remaining at Old Trafford and Mourinho was satisfied with the Frenchmans display off the bench.
I think Paul played well, Mourinho said following the draw.
The 15 minutes he was on the pitch he played well, in a moment where our defenders couldnt push up.
Every time David de Gea had the ball all my defenders were dead in front of him and I want the team to come up, I want the defensive line to push up, I want to play in the opposition half.
At that moment we have Fellaini, we have [Romelu] Lukaku, we have Paul, but every time David had the ball, everybody was dead.
When a reporter suggested that Uniteds players looked happier without Pogba in the starting XI, Mourinho replied: I dont understand where you want me to go. No. As I was saying, I think Paul came on and gave a good contribution and didnt give a bad contribution.
I brought freshness and power and different qualities to the attacking players but our defenders were dead. Was impossible to take them out.
David de Gea had the ball, waits two minutes for them, step by step to recover positions, or was kicking long.
When he was kicking long was Lukaku and Rashford against five Arsenal players. Our defensive players were completely dead.
And that made it more difficult to keep that happiness for the 95 minutes.