Twenty-six people have been jailed, including the chairman of champions Fenerbahce, who feature highly in the police investigation which has overshadowed preparations for the new season.
However, the Turkish Football Federation has said it will not launch its own probe until the indictment is prepared, effectively confirming Fenerbahce as champions for now and putting them into the lucrative Champions League group stages.
Trabzonspor finished second last season, meaning they go into the third qualifying round rather than qualifying directly for the group stage.
"We did our best, we got 82 points but we still didn't get the championship," Trabzonspor director Nevzat Aydin told Reuters.
"We should be at the group stage draw in Monaco, not here in Nyon. We deserve to be champions of Turkey under these circumstances."
Aydin said that Trabzonspor had six members questioned by police but that all had been released.
"I don't want to speculate because there are a lot of rumours, but the facts are that the president of Fenerbahce is in jail, the vice-president is in jail and the accountant is in jail," he added.
UEFA have said there is no reason to ban Turkish clubs from European competition on current evidence.
Before the draw, UEFA secretary Gianni Infantino reiterated UEFA's intention to heavily clamp down on match-fixing.
"In these uncertain times, with stories and rumours of match-fixing circulating across the continent, it is more important than ever to show respect for the game, for the officials, for your opponents and, most important of all, respect for the fans," he said.
"With new and tougher disciplinary regulations, we will not hesitate to come down very hard on any individual or individuals, clubs or officials that are proved to be involved in such illegal activities. Our policy remains zero tolerance."
Benfica, twice European champions, will play the first leg at home on July 26 or 27 with the return one week later.
In other ties, Danish champions FC Copenhagen, who last season became the first Danish team to reach the knockout stages, were drawn against either Shamrock Rovers of Ireland or Flora Tallinn of Estonia.
Scottish champions Rangers will face either Malmo - European Cup runners-up in 1979 - or HB Torshavn from the Faroe Islands and Dynamo Kiev take on Rubin Kazan from Russia.
