The Irish midfielder didn’t travel with the Dons on their flight to Slovenia, which eventually took off four hours late after a change of aircraft.
It’s a huge setback for Aberdeen. Hayes netted in the first leg and his drive caused the Slovenians all sorts of problems down the left wing.
Aberdeen manager Derek McInnes must now decide on a replacement, with on-loan Wes Burns an option in a match where the Scottish side have to score after a 1-1 first-leg draw at Pittodrie.
At a late press conference last night McInnes said: “Jonny picked up an injury in training yesterday, which was obviously a concern. It’s a blow. It’s one of these things we have to deal with because he’s a very important player.
“But we’ve dealt with playing without important players and still managed to get results. But there’s no doubt his pace in these games is really important.
“We tried to keep it quiet but these things never stay quiet. I think the opposition were aware of Jonny too and the threat he poses.
“It’s his hamstring, but we don’t know how long he will be missing for.”