Bolton moved to the brink of qualification from the Uefa Cup group stage after Gavin McCann scored the only goal at Red Star Belgrade.
McCann scored his first goal for Bolton on the stroke of half time
McCann struck from 12 yards on the stroke of half-time to leave Gary Megson's team top of Group F.
But three other teams could still finish ahead of Bolton dependent on scores in their final round of games.
Bolton keeper Ali Al Habsi saved from Joao Nuno Lucas and Ognjen Koroman, while Dejan Milovanovic shot just wide.
Megson's team, after three draws in their previous fixtures, have gone through the group stage unbeaten and finally have a victory to their name, to take their tally to six points.
But Bolton have played all four of their fixtures, while the other four teams in the group have one round of games left to play.
Bayern Munich and Aris Salonika could also move to six points if they draw next week, while Braga will also reach that total if they defeat Red Star, who have now lost the three games they have played.
That scenario would then see qualification come down to goal difference and then a series of criteria starting with goals scored to decide the three teams who will progress to the next stage.
Despite the significance of the match to the Trotters just four of the team that lost to Liverpool on Sunday - Nicky Hunt, Jlloyd Samuel, Abdoulaye Meite and Gavin McCann - started the match.
And with such a heavy pitch in Belgrade, Megson - clearly prioritising Premier League points - opted not to risk El-Hadji Diouf.
But the absence of players such as Nicolas Anelka, Kevin Davies, Kevin Nolan, Andy O'Brien, Ricardo Gardner and Jussi Jaaskelainen did not prevent Bolton ending the first half ahead when McCann struck after 45 minutes.
Their lead was in part attributable to the form of goalkeeper Al Habsi, who saved a 25-yard strike from Lucas with a dive to his left and a header from former Portsmouth player Koroman.
Milovanovic also threatened for the Serbian team with a free-kick that narrowly missed Al Habsi's goal.
A shot from Stelios deflected wide of the Belgrade goal off Christian Wilhelmsson, while the Swedish striker himself saw an effort miss after striking an opposition player.
Gary Speed, skipper for the night, shot wide but McCann was not to be denied after Red Star failed to clear a corner from Andranik Teymourian.
Stelios laid the ball into the midfielder's path and McCann scored his first goal for the club since joining last summer.
Bolton should have been two ahead when an unmarked Stelios connected with Andranik's free-kick after 52 minutes but the Greek could only guide the ball into the side netting.
Bolton manager Gary Megson on resting several senior players:
"I felt it was the right thing to do.
"Some players who were out there are internationals and have played big games in their careers.
"We knew they would be competitive and that's how it turned out."
Red Star Belgrade: Randjelovic, Bronowicki (Andjelkovic 80), Tutoric, Bajalica, Basta, Milijas (Burzanovic 73), Koroman, Lucas, Molina , Milovanovic, Jestrovic (Filip Djordjevic 64).
Subs Not Used: Banovic, Vladimir Djordjevic, Raskovic, Castillo.
Bolton: Al Habsi, Hunt, Meite, Michalik, Samuel, Giannakopoulos, Speed, Teymourian, Wilhelmsson, McCann, Braaten (Sinclair 87).
Subs Not Used: Walker, Guthrie, Harsanyi, Cassidy, Sissons, Woolfe.
Goals: McCann 45.
Ref: Paul Allaerts (Belgium).