Rory Gaffney had fired the Pirates ahead on the 31st minute, but the sides went into the break even when Jay Simpson tapped home his 18th of the season in first half stoppage time.
Eight minutes into the second half however Gaffney restored the hosts lead with a rasping shot into the bottom far corner.
On the back of their Boxing Day victory at home to Portsmouth the O’s made one change as Blair Turgott came in for the suspended Mathieu Baudry as the Frenchman served the first of a three-match suspension.
With both sides looking to end 2015 on a high it was the hosts who created the first chance of the match when Jermaine Easter tried his luck from the corner of the penalty area but Alex Cisak was equal to the effort as he parried it over.
Moments later Rovers’ Rory Gaffney beared down on goal having turned Connor Essam, but as the striker charged up a shot just inside the penalty area Cole Kpekawa came flying in with a stunning last-ditch challenge to deny him.
The O’s were struggling to create much going forwards and it was not until the 28th minute that they recorded their first shot on goal as Jobi McAnuff stung the hands of Rovers stopper Steve Mildenhall.
Three minutes later however the hosts made the breakthrough when Gaffney made the most of Essam missing a header and the forward then jinked his way past a number of Orient defenders before lifting a shot into the roof of the net.
Having taken the lead Rovers continued to dominate proceedings and with two minutes of the half remaining had a wonderful chance to make it 2-0 when Tom Lockyer got on the end of Lee Mansell’s free-kick, but the defender could only direct his header over the bar.
Lockyer’s miss was to prove costly however as for the second game running Orient scored in first half stoppage time as Jay Simpson popped up with yet another goal by getting on the end of Blair Turgott’s low ball across goal before tapping in.
Following the break Orient were forced into making one change as Frazer replaced Jean-Yves M’voto which saw Kpekawa move from left back to centre half alongside Essam.
Having claimed his 18th goal of the season just before the break, Simpson came close to making it 19 on the 50th minute when thread through by Bradley Pritchard, but Mildenhall was able to parry his powerful strike behind.
Soon after the O’s found themselves behind for a second time however when Lee Brown’s long ball forward found its way through to Gaffney who then sweetly struck a shot from the edge of the area beyond Cisak via the post.
In response to the goal Simpson and Turgott both had efforts held by Mildenhall before Gaffney was denied his hat-trick by the feet of Cisak having been played in by substitute Matty Taylor.
As the final 15 minutes approached John Marquis and Scott Kashket came on for Palmer and McAnuff, though it was Pritchard who was to come close to an equaliser on the 81st minute when he volleyed a shot just over the bar.
Despite throwing bodies forward for the final minutes, Orient were unable to force an equaliser as their final fixture of the calendar year ended in defeat.
BRISTOL ROVERS: Mildenhall, Leadbitter, Lockyer, Parkes, Brown, Bodin (J Clarke 74), Sinclair, Mansell (C), Montano (O Clarke 81), Easter (Taylor 67), Gaffney
SUBS: Preston, McChrystal, Gosling, Harrison
GOALS: Gaffney (31 & 53)
BOOKINGS: Sinclair (59), Parkes (65), Leadbitter (89)
ORIENT: Cisak, Clohessy (C), M’voto (Shaw HT), Essam, Kpekawa, Turgott, Payne, Pritchard, McAnuff (Kashket (73), Palmer (Marquis 73), Simpson
SUBS: Grainger, Dunne , Moncur, Adeboyejo
GOALS: Simpson (45+1)
BOOKINGS: McAnuff (63)
REFEREE: Kevin Johnson
ATTENDANCE: 9,836 (487 Orient fans)