Benfica - the first club Mourinho coached - had two goals disallowed on video review in the first half on Wednesday before their Turkish forward Kerem Akturkoglu scored with a rising shot in the 35th minute for the only goal over the two legs.
Club Brugge, Copenhagen and Qarabag of Azerbaijan also advanced to complete the 36-team line-up for the league phase.
Mourinho is a two-time Champions League winner but has not coached in the main stage of the marquee competition for six seasons. Fenerbahce's absence now stretches to 17 seasons.
Brugge routed Rangers 6-0 for an aggregate score of 9-1. The Belgian side already had an early lead before Rangers defender Max Aarons was sent off in the eighth minute.
Qarabag are back in the Champions League eight years after their debut campaign, winning 5-4 on aggregate over Ferencvaros despite a 3-2 loss in Baku on Wednesday.
Copenhagen won 2-0 at home to Basel to advance 3-1 on aggregate.
A total of 36 teams have qualified for the league phase of this season's competition.
Teams are divided into four pots. Each team will play against two others from each pot, with one match held at home and the other away.
Teams will be prevented from facing rivals from their own country and will be limited to playing against only two clubs from any single country.
The league-phase draw will take place on Thursday in Monaco, with the first matches to be played from September 16-18.
The final will be played on May 30 in Budapest, Hungary.
PROJECTED POTS:
Pot 1: Paris St Germain, Real Madrid, Manchester City, Bayern Munich, Liverpool, Inter Milan, Chelsea, Borussia Dortmund, Barcelona
Pot 2: Arsenal, Bayer Leverkusen, Atletico Madrid, Benfica, Atalanta, Villarreal, Juventus, Eintracht Frankfurt, Club Brugge
Pot 3: Tottenham Hotspur, PSV Eindhoven, Ajax Amsterdam, Napoli, Sporting CP, Olympiakos, Slavia Prague, Bodo/Glimt, Olympique de Marseille
Pot 4: FC Copenhagen, Monaco, Galatasaray, Union SG, Qarabag, Athletic Bilbao, Newcastle United, Pafos, Kairat
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