The defender is set to undergo surgery after sustaining the blow in the Dons’ 1-1 draw against Shkendija last week.
However, Dons boss Derek McInnes has backed summer signing Paul Quinn to slot seamlessly into his back four in Reynolds’ place for the return leg on Thursday.
Quinn, who joined from Ross County in the summer, replaced his former Motherwell team-mate in central defence in Skopje and could be set for an extended run in the team.
McInnes does have options, however, and could move Andrew Considine into central defence and slot Graeme Shinnie in at left-back.
He said: “Mark went to see a specialist yesterday and will get operated on on Friday in Glasgow. He will be out until the start of October certainly, 10-12 weeks.
“There’s a dislocation there but the severity of it means he requires an operation.
“Paul’s someone who, since he came in the door, has played and trained the way we expected him to. He brings a level of experience to the position and he’s a really good competitor.
“He came here to play and obviously Ash Taylor and Mark Reynolds have been a mainstay when they have been fit and available, but Mark’s disappointment is someone else’s opportunity.”
If selected, Quinn will need to be alert to deal with the counter-attacking threat of Shkendija at Pittodrie, a trait they displayed during a lively second-half display in the first qualifying-round opener.
McInnes said: “It’s getting the balance between patience and still generating the tempo and pace to the game.
“We know if we play with a certain energy we can be a far tougher opponent so it’s important we try to impose ourselves on the opposition, especially at home.
“I think we had relative control of the game and managed the game well enough last week, although there were two or three spells in the second half when they showed how dangerous they can be if we’re not fully concentrated.”
Aberdeen did not have their usual cutting edge in Macedonia but Niall McGinn grabbed a crucial away goal and McInnes feels they will be a lot sharper this time around.
“No matter how much training you do, or friendlies you play, however much you try to manufacture a competitive edge to training, nothing prepares you better than real football,” he said.
“It was good to get the first game played and since then the standard in training has been better again. The players that played have felt the benefit of that competitive match.”