It was the second time in a week that the Wanderers second string had found themselves on the wrong end of a 3-1 scoreline as West Bromwich Albion defeated the reserves last week at The Hawthorns.
The game had started brightly for Neil McDonald's side as Cleveland Taylor put the Wanderers ahead on nine minutes for what was his first goal of the season with a well taken finish.
United found themselves back on level terms on 29 minutes when midfielder Andrew Keogh swept home a loose ball in the area after the Bolton keeper Jeremy Bon had failed to keep hold of Craig Stiens initial shot.
Both sides went in level at the interval but two goals by the away side in the second half saw the inexperienced Bolton side crumble as just two minutes after the restart Martin Woods had put Leeds ahead from the penalty spot after a handball offence.
And with just ten minutes remaining midfielder Simon Johnson scored the best goal of the game as his 25-yard drive past Jeremy Bon gave Steve Agnew's youthful Leeds side the win but added more concern for the Wanderers who have just won one in ten league games in the reserves.