The Lions took the lead just after 10 minutes, when good work by Regan Hutchinson led to a cross into the area, that was headed onto the bar by Jordan Thewlis and Lewis Hey had a simple tap-in to give the hosts the advantage.
A penalty was conceded just before the half-hour mark, when Hamza Bencherif brought down Lee Ndlovu, Matt Lowe stepped up but his shot was always going wide.
Guiseley started the second-half brightly and Bencherif nearly doubled their advantage as headed towards goal, with the effort going just over the bar and away.
The visitors drew level soon after, a well-worked move saw Ndlovu placed through on goal one-on-one and he made no mistake with a calm finish.
What is happening to former Leeds United star Raphinha at Barcelona amid latest farce and deadline
Leeds United news: Raphinha set to miss La Liga opener as Whites eye MLS left-back
Leeds United ‘express interest’ in transfer as ‘decision made’ over player’s future
Leeds United in ‘direct talks’ over swoop for rising star as Jesse Marsch makes ‘transfer decision’
Leeds United plot ‘double hit’ for attacking duo, Whites ‘weighing up’ bargain defender swoop
Guiseley nearly got back infront immediately as Jamie Spencer on the edge of the area, but his shot hit off Mbeka and was eventually cleared.
It looked like there might be extra-time but a pinpoint cross found Mbeka who powered a header past Danny Lewis and into the goal for the winner.
The Lions will next face League 1 AFC Wimbledon away from home inthe first round.
Jack Vale’s first goal for The Shaymen saw FC Halifax Town beat a plucky Pontefract Collieries 1-0 in the fourth qualifying round of the FA Cup.
Town will now play Maidenhead in the first round thanks to substitute Vale’s second-half winner.
York City are also through to the first round after Kurt Willoughby’s hat-trick saw them earn a 3-1 replay win over hosts Morpeth Town
Harrogate Town earned a point of the ‘good’ variety on Tuesday evening, playing out a thrilling 2-2 draw with fellow League Two high-flyers Tranmere Rovers.
Goals either side of the interval from Jack Muldoon and Luke Armstrong saw the Sulphurites recover from a Jay Spearing penalty down to seize the ascendancy early in the second half, but the visitors levelled soon afterwards through Kieran Morris’ header and in the end, the spoils being shared was probably a fair outcome.