It was James Brophy who had unfortunately turned the ball past his keeper to give Bolton the lead, before Eoin Doyle made sure of the win with a strike two minutes later.
The O’s handed a full debut to recent signing Dan Kemp, whilst Hector Kyprianou earned a position in midfield at the expense of Ouss Cisse.
Dan Happe served the first of a two game ban, so Josh Coulson partnered Tunji Akinola – whilst Lee Angol missed out with injury.
Bolton, keen to avenge the 4-0 defeat back in October, nearly had the perfect start, as Gnahoua found Delfouneso unmarked in the penalty area, which just nine minutes played.
The ex-Blackpool man couldn’t convert though, and from close range Lawrence Vigouroux was able to pull off a fantastic reflex stop.
Jobi McAnuff looked to recreate his effort in the reverse fixture with a free-kick from 25 yards, but his strike wasn’t troubling Gilks.
The hosts looked the most likely to break the deadlock in the first half, and Eoin Doyle perhaps came closest, with his effort from distance forcing Vigouroux into another save.
As half-time approached, The Trotters had a flurry of efforts but again the O’s held firm, and the interval came as a welcome respite.
The second half saw Orient start with more fluency, and certainly started as the side on top – with Dan Kemp and Hector Kyprianou firing efforts from distance to test Matt Gilks.
With the game delicately poised, Head Coach Ross Embleton opted to make the first change, with Joe Widdowson replacing Dan Kemp – and James Brophy moving into an advanced position.
And this nearly proved the catalyst for The O’s, as James Brophy’s pinpoint free-kick found Ruel Sotiriou in the box – but the striker headed wide from close distance, and perhaps Orient’s best chance went begging.
The fine margins of football were soon displayed once again, as Bolton’s next attack saw them break the deadlock.
Lloyd Isgrove drove forward and drilled a cross low into the back post, and with Harry Brockbank lurking, James Brophy was forced to try and clear it from under the crossbar.
Brophy’s attempt however was in vain, and instead, he saw his clearance hit the back of the net, and Orient were trailing.
This misery was soon compounded, as Arthur Gnahoua’s pass found marksman Eoin Doyle in the box, who doubled the Trotters’ lead with a smart, low finish.
Orient responded with the introduction of Nick Freeman in midfield, and later James Dayton – and a big chance fell to Conor Wilkinson to half the deficit.
Wilkinson, however, fired his effort high over the bar, and with it went Orient’s chances of a late comeback.
Bolton themselves could have had another goal in injury time, as Nathan Delfouneso fired over from 18 yards.
The final whistle eventually came after six minutes of injury time, and Orient’s journey home from the north west was to be done empty handed.
Bolton Wanderers: Gilks, Santos, Delfouneso, Doyle ©, Brockbank, Isgrove (Elbouzedi 79’), Gnahoua, Thomason, Baptiste, Lee, Jackson (John 80’)
Subs unused: Jones, Comley, Crawford, Greenidge, Tutte.
Goals: Brophy O.G 67, Doyle 69’
Leyton Orient: Vigouroux, Ling, Coulson, McAnuff ©, Clay (Dayton 80’), Wilkinson, Brophy, Akinola, Sotiriou, Kyprianou (Freeman 76’), Kemp (Widdowson 59’)
Unused substitutes: Sargeant, Cisse, Turley, Sweeney.