Dean Cox's first-half strike was enough to guide the O's into the next round of England's most prestigious cup competition and took his personal tally on to double figures for the season.
Walsall had the better chances in the opening period but Cox gave the home side the advantage on 41 minutes when he created some space for himself inside the opponents' box and sent a powerful effort flying into the top corner.
A finely balanced second half saw neither team able to add to the scoresheet however, in a fiery conclusion to the game, Orient captain for the day David Mooney was shown a straight red card for lashing out at Walsall's Paul Downing.
Orient boss Russell Slade was struck down with a bug and was therefore unable to be at the match, meaning his trusted assistant manager Kevin Nugent took charge of the team.
The O's manager was not the only key member of staff missing for the FA Cup tie as captain Nathan Clarke was also forced to sit out due to a groin injury and fellow defender Scott Cuthbert was not fit enough to make the squad.
With Clarke missing, Orient top scorer Mooney was handed the captain's armband for the first time, while Gary Sawyer and Yohann Lasimant were drafted into the starting XI.
With Kevin Lisbie still sidelined with an ankle injury and loanees Marvin Bartley and Josh Wright ruled out from playing in cup games, Orient's relatively small squad was so stretched they could only name six substitutes - one of which was first year scholar Sam Ling, son of ex-O's boss Martin.
Walsall, who were visiting Brisbane Road for the second time this season after securing a point against the O's in the league back in September, made three changes to the side that lost to Port Vale in the league last week with Ben Purkiss, Nicky Featherstone and Ashley Hemmings all returning to the starting XI.
Orient started the game on the front foot but Walsall forward Craig Westcarr was the first to force either keeper in to action when he broke the offside trap and brought a flying save out of Jamie Jones. And from the resulting corner visiting skipper Andy Butler, who was sent off the last time these sides met, sent a volley from the edge of the area narrowly over the bar.
The home side's passing was nowhere near as crisp or accurate as it has been so far this season and this made for a scrappy opening half an hour, during which the O's managed to create just one good opportunity when Shaun Batt played in strike partner Mooney only for the stand-in captain to skew a left-footed effort high and wide of the target.
Meanwhile Walsall looked far more dangerous when they entered the final third, with Hemmings and Westcarr each sending curling efforts inches wide of either post.
However Orient found the clinical edge that they have carried with them all season on 41 minutes when Dean Cox fired them ahead with his third goal in as many games.
Mooney sent a low ball across the box which evaded everyone until Cox got on the end of it to turn inside and smash a shot directly into the top right-hand corner. It was the only section of the target he was guaranteed to find the back of the net with as there was a cluster of players inside the six yard box blocking his path to goal.
And the winger's 10th goal of the season was the last significant action of the first half, giving the O's a slender advantage at the break.
The start of the second period followed the same fashion as the first, with Orient seeing more of the ball but Walsall managing to come closest to scoring when Hemmings got in front of his man to poke a close-range shot goalwards but Jones was again alert and got down well, crucially holding on to the ball.
Westcarr had looked the most dangerous man for the opposition all afternoon and he came one step closer to adding to his nine goals this season shortly after the hour mark when his bending free-kick struck the post and, luckily for Orient, rebounded off of Jones's back and away from danger.
The O's front men had struggled to break the away side's offside trap all afternoon but the linesman kept his flag down midway through the half when Batt raced in behind the Walsall defence only to drag a shot wide with his weaker foot.
Orient used all three substitutes in the second half, and the fresh legs together with a change of shape to 4-5-1 late on kept the visitors at bay.
In fact, great link up play down the left flank between two of the replacements, Johnny Gorman and Harry Lee, could have seen the O's add to their advantage with four minutes left on the clock but the former drilled a decent effort into the side netting.
What had been a relatively tame game descended into chaos in second half stoppage time when referee Mark Brown was forced to make his first bookings of the game and gave Mooney his marching orders.
The Orient skipper and Walsall defender Paul Downing picked up a yellow card each for a coming together in the 93rd minute and 90 seconds later, Mooney was shown a straight red for lashing out at the same opponent.
It was a sour note to end his first 90 minutes wearing the captain's armband and he had put in a good performance but the O's top scorer could have no complaints with his punishment.
Nevertheless, it was a successful afternoon's work for the home side, securing their place in the draw for the third round of the FA Cup alongside the biggest clubs in the country.
ORIENT: Jones, Odubajo, Omozusi, Baudry, Sawyer, Lasimant (Gorman, 75), James, Vincelot, Cox (Simpson, 60), Mooney (C), Batt (Lee, 85).
SUBS NOT USED: Larkins, Finney, Ling.
GOALS: Cox (41)
BOOKINGS: Mooney (90+3)
REDS: Mooney (90+5)
WALSALL: O'Donnell, Purkiss, Taylor, Butler (C), Featherstone (Sawyers, 62), A.Chambers, Mantom, Lalkovic (Baxendale, 71), Westcarr, Hemmings (Hewitt, 82), Downing.
SUBS NOT USED: Lewis, Benning, J.Chambers, Gray.
BOOKINGS: A. Chambers (90+2), Downing (90+3)
REF: Mark Brown
ATTENDANCE: 2,604 (259)