It would have been difficult for any outsider to tell which team was in the higher league as Luton Town bossed proceedings for the opening 45 minutes.
The second half saw a more equal game, but despite continuing to put pressure on the defence it took 88 minutes before the Hatters took a well deserved lead, putting them through to the Southern Area Semi-Finals of the Johnstone's Paint Trophy.
Rossi Jarvis scored for Luton after Chris Martin saw his initial attempt saved by the Walsall keeper.
The Hatters made one change to the starting line up following their 3-0 defeat at Shrewsbury last weekend. George Beavan, who has returned from Salisbury where he was on loan, replaced Harry Worley.
Additions to the bench were Kevin Watson and Garreth O'Connor, who have both returned from injury.
Claude Gnakpa almost put the Hatters ahead on 12 minutes when his header forced an impressive save from keeper Clayton Ince following a well placed Jake Howells corner.
In the 16th minute a long ball opened up space for Chris Martin who passed the defence to go one on one with the keeper. Unable to get a clear shot, Martin flicked the ball back to the onrushing Rossi Jarvis who fired the ball towards the top right-hand corner, but the Walsall keeper pulled out another great save to deny the Hatters again.
Luton continued to pile on the pressure and Captain Keith Keane tried his luck from 25 yards in the 19th minute but saw his attempt flash wide.
Another great long ball from Paul McVeigh allowed Tom Craddock to rush past the defence before passing the ball back to Martin who was unfortunate to see his curling right-footed shot clip the crossbar.
It took the League One side 34 minutes to make an attempt at goal. Chris Palmers' cross gave Michael Ricketts the opportunity to put the home side ahead but his header didn't trouble Conrad Logan as it sailed over the crossbar.
HALF-TIME: WALSALL 0-0 LUTON TOWN
A mistake in defence on 51 minutes allowed Ricketts to slip through, but the undeterred Logan came off his line to produce a great save.
A cross from the right caused problems in the Hatters area just minutes later when Ricketts headed the ball powerfully towards goal but on loan keeper Logan managed to get a fingertip to it to once again deny the Saddlers.
Troy Deeney could have put Walsall ahead on 67 minutes but his header flew over following a well placed cross from Anthony Gerrard.
Craddock's shot in the 71st minute looked to have beaten the keeper, but much to the disappointment of the away fans, went narrowly wide.
Emotions began to run high as both sides tried desperately to prevent the game going to penalties, and both Spillane and Jabo Ibehre were lucky not to be sent off when the two players entered into a confrontation.
With just three minutes left to play substitute Garreth O'Connor had his first attempt of the game spectacularly denied by Ince.
On 88 minutes, the Hatters finally made the breakthrough that their dominance deserved. After a quick counter attack Martin saw his shot deflected, but Rossi Jarvis was on hand to fire home the loose ball, giving the Hatters the lead.
FULL-TIME: WALSALL 0-1 LUTON TOWN
Walsall: Ince, Taundry, Boertien (Nicholls 67), Hughes, Gerrard, Roberts, Mattis, Deeney (Zaaboub 84), Ibehre, Ricketts, Palmer
Subs not used: Gilmartin, Smith, Bradley
Bookings: Gerrard (56), Ibehre (81)
Luton Town: Logan, Gnakpa, Howells (O'Connor 46), Roper (Worley 53), Spillane, Jarvis, Keane, McVeigh, Beavan, Craddock (Watson 90), Martin
Subs not used: Brill, Andrews
Bookings: Spillane (81)
Referee: D Deadman
Attendance: 1,844 (153 from Luton)
