Fejsa, who had a good first half in Friday's 1-1 home draw against Italy, limped off at the interval with an ankle injury while Manchester United centre-back Vidic is unfit after struggling with a calf injury since August.
"I don't think Fejsa will go with us to Slovenia on Sunday, we had to substitute him at halftime after he hurt his ankle," Petrovic told reporters after Serbia recovered from falling behind in the first minute.
"Vidic is our best defender and we sorely missed him against the Italians, but it is highly questionable how much we can use him in Slovenia because of his physical condition.
Serbia, who could have clinched a play-off berth with a win over Group C winners Italy, must now beat eliminated Slovenia to finish second ahead of Estonia, who leapfrogged them into the runners-up spot with a 2-1 win in Northern Ireland.
The Estonians have played all their games and will now hope that Slovenia will do them a favour in a match where pride will be at stake against their fellow former Yugoslavs.
Manchester City left-back Aleksandar Kolarov said: "In a way it will be easier than all the other qualifiers in this campaign because there is no more room for calculation, it's make or break.
"I am very surprised with the jeers by some fans in the closing stages against Italy, we don't have the makings of teams like Brazil so people shouldn't expect us to beat rivals like Italy by a 3-0 scoreline."
The Serbs had more chances in a pulsating match at Red Star Belgrade's Marakana stadium but found it difficult to carve openings with a conservative 4-2-3-1 formation.
Petrovic, who threw on three forwards in the last 10 minutes, is likely to field a more adventurous 4-4-2 against the Slovenians, with either striker Nikola Zigic or left forward Milan Jovanovic up front alongside Marko Pantelic.
With midfielder Zdravko Kuzmanovic also sidelined with a long-term injury, Petrovic has few options in the engine room and Radosav Petrovic looks like the only natural replacement for Fejsa.
