The Serie A side had no substitutions left having made eight at the Air Albania Stadium against Partizani Tirana in their eventual 2-1 win.
Still, in the 79th minute, Mourinho hooked summer signing Auoar from the pitch, while the hosts were playing out from the back.
The ex-Lyon midfielder could be seen walking towards the ex-Chelsea manager on the sidelines with a confused look on his face.
Mourinho put his arm around the 25-year-old and explained his reasoning as the Frenchman simply trotted to the dugout to take his seat on the bench.
And according to Corriere dello Sport, there were two key factors as to why the 60-year-old came to his decision.
READ MORE ON SERIE A
Loftus-Cheek nets first-half hat-trick for Milan with help from ex-Chelsea star
Hugo Lloris 'in negotiations' with Serie A side over free transfer from Tottenham
Living up to his Special One nickname, the Italian news outlet has stated that Mourinho took Aouar off to level up the game at ten men all.
Partizani manager Zoran Zekic was claimed to have made an error in the second half, as he brought a player off to replace him with someone he had already taken off.
The referee turned down the request, leaving the hosts with a player less than Roma, with Mourinho countering by removing Aouar.
But that wasn't the only reason for his withdrawal, with Mourinho subbing out the former Arsenal target to avoid him from suffering an injury.
Most read in Football
Kane speaks to media, Chelsea hopeful of Caicedo hijack, Man City set up Paqueta pursuit
Tottenham summer signing replaces Harry Kane as the club's new No.10
Thomas Tuchel says sorry to Harry Kane as Bayern Munich debut ends in misery
Mbappe all smiles as he joins Dembele to watch PSG struggle in Ligue 1 opener
It has been said that Aouar was getting targeted by the Partizani players having been on the receiving end of some tough challenges.
Partizani did manage to halve the deficit when Aoaur went off, but Roma held on for the win ahead of the start of the new Serie A season.
Roma kick off their campaign against Salernitana next Sunday as they look to better their sixth-placed finish from last term.