The Hatters took the lead through Danny Hylton and led at the break only for the Liam Kelly to level from the spot.
Tristan Abrahams put the O’s ahead with his first senior goal, but Omer Riza’s side were denied the three points through substitute Isaac Vassell’s effort.
The O’s made four changes to the team which lost out 3-0 at Cambridge United last weekend with Henry Ochieng coming in for his first start on the left of a midfield diamond, while Teddy Mezague returned from injury, with Sam Dalby and Victor Adeboyejo partnered up top.
The early stages saw Luton dominate possession, but failed to test Sam Sargeant as both sides settled into the game.
Lawson D’Ath headed the first real opportunity of the game wide from Alan Sheehan’s wicked cross from the left, before the Hatters won their first corner of the afternoon.
Orient produced their first foray forward into the Hatters box with 14 minutes on the clock and it almost proved profitable when Michael Collins’ cross from the right found the header of Adeboyejo but he directed it over the bar.
Luton began to pressure the O’s goal and former Orient defender Scott Cuthbert saw a header blocked before the ball fell back to him and it was deflected over.
Set pieces have been one of Orient’s weaknesses and this time Rea was able to rise highest to head Cook’s corner goalwards, only to direct the header straight at Sargeant.
But the deadlock was broken on 32 minutes when an Olly Lee ball over the top found the run of Danny Hylton who beat the offside trap and despite a desperate attempt from Semedo to get back, he slotted past an onrushing Sargeant to give the hosts the lead.
Sargeant was called into action again to hold a fierce effort from Lawson D’Ath after Alan Sheehan’s free-kick hit the wall, before substitute Luke Gambin’s ferocious strike was well tipped over by the young goalkeeper.
He was at it again to deny the same man once again, this time from the left hand side of the box.
Just as the half was drawing to a close the Hatters had one more opportunity to double their lead when Marriott produced a neat turn and shot on the edge of the box but he directed the effort just over the bar.
Riza made one change at the break with Tristan Abrahams replacing Sam Dalby and it was O’s who had the first chance of the half when Collins’ low free-kick forced Stuart Moore into his first real save of the game.
That lifted the O’s and Adeboyejo tried his luck with a fierce effort from 30 yards out but Moore was able to hold in the Hatters goal as the home crowd starting to getting on the back of the Hatters players.
But Orient had a lifeline on 53 minutes when Glen Rea was adjudged to have handled Collins’ fierce effort and referee Brett Huxtable pointed to the spot.
Captain Kelly stepped up to take the penalty and he fired high into the roof of the net to level matters for Riza’s side.
Luton went back on the attack and Sheehan fired an effort across goal just wide as the hosts looked to restore their lead, but to no avail.
Orient kept going though and Kelly saw a goalbound effort blocked after the ball fell to him on the edge of the box as they sensed a second.
And that came when the ball arrived at the feet of Abrahams on the right after a lovely ball through from captain Kelly and the striker slotted home his first goal for the O’s senior team and he celebrated in style in front of the 380 Orient fans who made the journey to Kenilworth Road.
It almost got even better for the O’s when Kelly headed the ball through for Abrahams and though the ball never fell right for him, the ball almost found its way to Adeboyejo only for Moore to come out and gather.
That proved costly though as the hosts levelled with 17 minutes remaining as a ball through found Vassell who paced clear of the defence before slotting into the far corner past an onrushing Sargeant.
Chances continued to come for both teams and O’s still looked a threat on the counter while the hosts threw everything at the O’s and Sargeant did well to come out and gather at the feet of Rea.
Time continued to tick away and the hosts saw two penalty appeals waved away as Mezague and Vassell came together in the box, before five minutes stoppage time was announced.
There was still time for a late chance for the O’s as the ball broke to Koroma but it got tangled up under his feet and the attempt was blocked behind for a corner.
It was Orient who looked the likelier to score deep into stoppage time but Huxtable blew his whistle and the O’s had picked up a battling and deserved point despite the adverse conditions surrounding the club.
LUTON TOWN: Moore, Sheehan, Rea, Cuthbert, Justin, Ruddock-Mpanzu (Gray 85), Lee, Cook (Gambin 24), D’Ath, Marriott (Vassell 66), Hylton
SUBS: King, O’Donnell, Potts, Smith
GOALS: Hylton (32), Vassell (73)
BOOKED: Gambin (44), Rea (53), Cuthbert (81)
LEYTON ORIENT: Sargeant, Semedo, Mezague, Pollock, Clark, Ochieng (Moncur 88), Kelly, Collins, Alzate (Koroma 80), Dalby (Abrahams HT), Adeboyejo
SUBS: Grainger, Liburd, Alderson, Happe
GOALS: Kelly (54 pen), Abrahams (61)
BOOKED: Ochieng (67), Sargeant (73)
REFEREE: Brett Huxtable
ATTENDANCE: 8,601 (380 Leyton Orient fans)