Pafos endured nearly 10 minutes of added time following Jaja’s late goal that leveled the score.
Pafos FC of Cyprus and Norway’s Bodo/Glimt are set to make their Champions League debuts this season, having successfully navigated the qualifying play-offs.
Founded just 11 years ago, Pafos secured a 1-1 draw against Red Star Belgrade on Tuesday, clinching a 3-2 aggregate victory.
Bodo/Glimt also advanced to the league phase, overcoming Austrian side Sturm Graz with a 6-2 aggregate score, despite a 2-1 defeat in the second leg.
The two clubs will join Kairat Almaty of Kazakhstan, who delivered a stunning defeat to Celtic via penalties, and Belgian champions Union Saint-Gilloise, all making their inaugural appearances in Europe’s premier club competition.
Pafos commenced their continental campaign in the second qualifying round on July 22, defeating Maccabi Tel Aviv and Dynamo Kyiv en route to the play-offs.
Holding a 2-1 advantage from the first leg, Brazilian winger Jaja scored in the 89th minute of the return match in Limassol, equalizing after Mirko Ivanic had put Red Star ahead.
The Cypriot champions, who recently signed 38-year-old former Chelsea and Arsenal defender David Luiz, will become only the third club from Cyprus to participate in the Champions League, following Apoel and Anorthosis Famagusta.
Bodo/Glimt, a four-time Norwegian champion, is the first club from Norway to reach the competition proper since Rosenborg in the 2007–08 season.
The club, located 200km north of the Arctic Circle and playing at the 8,270-seater Aspmyra Stadion, gained prominence last season by reaching the Europa League semi-finals, where they were defeated by eventual champions Tottenham.
Kairat, who narrowly defeated Scottish champions Celtic in a penalty shootout after goalless draws in both legs, becomes the second Kazakh side to qualify for the competition after Astana in 2015–16.
The journey to Almaty in central Asia could present a significant challenge for Kairat’s European opponents, as Chelsea undertook a 3,600-mile trip to the city last season to face Astana en route to winning the Uefa Conference League.
The draw for the league phase of the Champions League is scheduled to take place on Thursday in Monaco, with the first matchday set to occur between September 16 and 18.
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Catch highlights of every Champions League game from 22:00 on Wednesday on BBC iPlayer and the BBC Sport website and app.
Additionally, a Champions League Match of the Day program will air on BBC One on Wednesday, from 22:40 to 00:00.