Bothroyd had been doubtful with a leg injury but started the second half when he replaced Carl Cort.
There seemed no danger to the Leeds defence when Bothroyd got the ball 20 yards out, but he produced an unstoppable shot past Tony Warner's left shoulder into the far corner of the net.
Before then Matt Murray, the former England Under-21 goalkeeper, had kept Wolves in the game with a spellbinding save.
Murray, whose career has been hampered by a series of injuries, showed his class when Leeds' French winger Seb Carole seemed a certain scorer in the 37th minute of a keenly-contested encounter.
Stephen Crainey, Ian Moore and Jonathan Douglas created the opening for Carole who burst through and couldn't believe his bad luck when Murray showed lightning reactions to sprint across his line and beat out the shot.
Murray had earlier sprung to the rescue by saving from the lively Moore at the near post. However, he spread panic among his defenders when he mishandled a shot from Leeds captain Paul Butler and then almost let in substitute Steve Stone after missing a cross.
Leeds had Douglas making his first appearance since joining them on a permanent deal from Blackburn after spending most of last season at Elland Road on loan.
Charlie Mulgrew came in at left-back for Wolves in place of Jamie Clapham, who was ruled out by a groin strain, but the ex-Celtic man struggled to stem the pace of Carole and was substituted just before half time.
Leeds created the better opportunities and it needed a goal-line clearance from Karl Henry to keep out Matthew Kilgallon's header from Gary Kelly's cross.
United substitute Jermaine Beckford, who replaced Moore in the 77th minute, made an immediate impact, Jodie Craddock almost turning the youngster's right-wing cross into his own net.
Leeds were hoping David Healy could continue his goal exploits after his hat-trick for Northern Ireland against Spain in midweek but there was to be no repeat.