The first half-chance of the match arrived after six minutes when Wolves midfielder Kevin McDonald found some space outside the box, but his curling effort went straight into the body of Orient stopper Jamie Jones.
The visitors were ahead after 17 minutes when Richard Stearman appeared at the far post to head his second league goal of the season past Jones from close range.
Wolves continued to threaten as the half gathered pace, with Bakary Sako bringing a smart save from Jones after 25 minutes.
Orient's best chance of the match arrived moments later, however, when Mathieu Baudry met a cross from the left, but his header just dropped over the Wolves crossbar.
The home side felt they should have had a penalty 15 minutes before the interval when Stearman stuck out a hand inside the box, but the referee waved play on, much to the frustration of the majority inside Brisbane Road.
Minutes later, Wolves had their second when Sako broke into the box before finding the back of the net via the post.
Orient again came close in the latter stages of the half when Dave Mooney dribbled into the Wolves box, but Carl Ikeme was on hand to make a smart save, before the stopper denied a powerful header from Nathan Clarke as Orient ended the half on top.
Ikeme was twice called into action in the opening moments of the second period, but the experienced stopper answered the call on both occasions to deny Chris Dagnall and then Mooney from close range.
Orient's pressure paid off after 47 minutes, however, when Dean Cox placed one into bottom corner inside a crowded box.
Wolves had the chance to regain their two-goal lead 10 minutes later when Sako found some space inside the Orient box, but his low effort just whistled wide of the post.
Mooney might have levelled after 62 minutes after meeting a loose ball inside the area, but the striker lifted his effort over the top of the crossbar in an end-to-end period of the match. Dave Edwards then came close for Wolves with little over 20 minutes remaining, but once Jones made the save.
Orient hit the crossbar in their next attack through Shaun Batt, before Ikeme clawed clear following a period of pin-ball inside the Wolves box.
The home side continued to press in the latter stages, but it was Wolves that scored a third in stoppage time when James Henry rattled in his 10th league goal of the season to move the club onto 99 points.
Mathematically, Wolves are still not the champions, but it would take a remarkable swing in terms of points and goal difference for Brentford to catch the former Premier League side at the summit.