The Turkish league runner-up had been excluded by UEFA, but reached agreement on Thursday at the Court of Arbitration for Sport to freeze the sanction and play before its appeal is judged next month.
In some of the other 15 drawn pairings, Zenit St. Petersburg will play Nordsjaelland, 1988 winner PSV Eindhoven faces Champions League debutant Zulte Waregem of Belgium, and Metalist Kharkiv will travel to play PAOK Thessaloniki of Greece.
Fenerbahce officials declined to discuss the 18-time Turkish champion's legal problems at UEFA headquarters.
Still, the uncertainty involves Salzburg, a potential playoff round opponent next month — including Arsenal or AC Milan — and Turkish league rival Bursaspor, which was on standby to take the vacant place in the draw.
"Of course, we are a little bit confused about things that happened yesterday," Salzburg official Mark Lang told The Associated Press. "We don't have any influence on these decisions."
CAS set an Aug. 28 deadline — the eve of the group-stage draw — to give a verdict in Fenerbahce's appeal against a two-year ban from UEFA competitions. Club officials were convicted in a Turkish criminal court of helping to fix matches to win the Turkish title in 2011. They deny wrongdoing and have appealed.
Still, the Turkish Football Federation withdrew Fenerbahce just before the 2011-12 Champions League groups draw, and UEFA reinstated Trabzonspor, which had lost in the qualifiers.
If Fenerbahce wins through to the group stage yet loses its legal challenge at CAS, UEFA must decide which team would take its place in the 32-team draw in Monaco.
The simplest solution is for Salzburg to win a two-leg series which opens in Austria on July 30 or 31, and concludes in Turkey on Aug. 6 or 7.
"We are trying to beat them on the field," Lang said. "It's a very interesting opponent, and we're looking forward to the matches."
Bursaspor officials, attending the subsequent Europa League draw, acknowledged having no idea if their club could yet be upgraded to Europe's marquee club competition.
PAOK was also affected, because Fenerbache's reinstatement as a seeded team knocked the Greek league runner-up down into the pool of unseeded clubs.
PAOK will host Metalist in an empty stadium, as the club serves a UEFA ban for crowd violence in a Europa League match last season.
Ukrainian runner-up Metalist has finally broken through into the Champions League by finishing behind champion Shakhtar Donetsk, pushing longstanding power Dynamo Kyiv into third.
"Champions League is a big challenge," Metalist official Anton Ivanov told The AP. "We were looking for it for a lot of years. To play in the group stages, we need to beat teams like PAOK. It's a big advantage that PAOK plays without spectators."
Winners advance to a playoff round, when the non-champions in Friday's draw will be joined by Arsenal, Milan, Schalke, Real Sociedad and newcomer Pacos de Ferreira from Portugal.
The 10 playoff winners advance to the groups with the established European powers who have direct entry. Group matches start in September.