Brentford’s 2-2 draw with MK Dons later on Monday ensured that the Molineux club could celebrate their promotion as champions.
It took the visitors only 16 minutes to break the deadlock when Richard Stearman found himself unmarked at the far post to head home a corner following a flick-on from Danny Batth.
Orient had a penalty appeal for handball by Stearman turned down before the visitors doubled their advantage on 33 minutes when O’s defender Matthieu Baudry carelessly gave the ball away and Bakary Sako fired into the corner of the net.
Orient improved after the interval and Dean Cox gave them a lifeline within two minutes of the restart when his well-placed shot eluded Carl Ikeme in the Wolves goal.
Ikeme then produced saves to deny Mooney and Cox and was grateful to his crossbar for keeping out a Shaun Batt effort.
However, substitute James Henry put the issue beyond doubt in stoppage time when he fired home from 25 yards.