Leeds could have got their noses in front as early as the third minute but Barry Corr saw his penalty kick hit the crossbar but the young striker atoned for his error a quarter of an hour later when putting the home side one goal to the good.
Ricky Shakes, who is being linked with a move to Burnley, had the Trotters best chance of the half but could not get enough direction on his long range effort to test the Leeds goalkeeper Paul Harrison.
Within five minutes of the re-start Nigerian international Blessing Kaku had brought the Wanderers back into the game from the penalty spot after striker Bedi Buval had been impeded by Harrison.
Ten minutes later Polish centre back Jaroslaw Fojut hit the winning goal for Bolton with a fine header from a Reda Kribib corner kick. Kribib himself could have got on the scoresheet thereafter but his long range attempt could only come thundering back off the crossbar.
New signing Vincent Candela lasted an hour of the game and was replaced by Welsh youth international full back Rhys Powell.
BOLTON RESERVES: Andy Oakes, Vincent Candela (Rhys Powell), Jason Talbot, Florent Laville (Danny Stott), Jaroslaw Fojut, Dale Whitehead, Blessing Kaku, Bradley Hill (Karl Luisi), Bedi Buval, Ricky Shakes, Reda Kribib.
SUBS NOT USED: Chris Howarth, Craig Knowles.
LEEDS RESERVES: Paul Harrison, Simon Madden, Ben Parker, Matthew Spring, Stewart Edwards, Paul Keegan, Seth Johnson, Eirik Bakke (Nick Gray), Barry Corr (Morris), Gavin Rothery (Harpal Singh), Martin Woods.
SUBS NOT USED: William Coyles, Leister.