The 23-year-old received a three-match ban for kicking at an opponent off the ball during the home encounter with Real Betis in October.
The first game he missed was the reverse fixture against Betis, before also sitting out for the HJK clash.
Roma sent a request to UEFA asking the body to reduce his ban to only two games. UEFA acquiesced and will now allow the Italy international to play against Ludogorets.
Mourinho will need to wait and see, as Zaniolo picked up a knock against Hellas Verona in the Serie A on Monday.
Zaniolo has scored one goal and provided one assist in his 10 appearances across all competitions this season.
The Giallorossi must beat Ludogorets to qualify for the Europa League play-offs.