A free-kick to the far post found, found Theo Vassell who scored with a tap-in.
Guiseley boss Paul Cox said: “It was a performance with many positives, but we have switched off right at the end and lost it, you can’t do that or you are punished and that’s what happened.”
This game had been postponed twice in the last few days due to a frozen pitch, but despite a chilly night the game took place.
Guiseley should have been awarded a penalty when new signing James Roberts on loan from Oxford United was brought down in the area but nothing awarded.
The hosts had chances with ex Lion Jordan Preston forcing a smart save from Jonny Maxted.
Gateshead though did take the lead, when ex FC Halifax Town man Richard Peniket placed an effort into the bottom right hand corner.
The visitors went with an attacking formation that saw three strikers on the pitch, with Rowan Liburd producing a strong run but his cross just past the other forwards.
Guiseley had the better of the second half and soon equalised when an Alex Purver through ball found Liburd who did well to power an effort in from six yards out.
There was a fine chance for Guiseley when Connor Brown put a cross in towards the face of goal, but Raul Correia couldn’t make contact.
This stalemate was not to be broken in the 90 minutes, so it went to extra-time.
Gateshead had the best chance of the first half of extra time when Peniket forced a save off Maxted, but both sides were tiring.
Chances were then few and far between, before Vassell won it.
Gateshead: Montgomery, Tinkler, Byrne, Kerr, Barrow, Peniket (O’Donnell 110) Penn, Williams (Vassell 103) Preston (York 84) Johnson, Burrow. Unused substitutes: Vassell, Fyfield, Macleod
Guiseley: Maxted, Palmer, Lawlor, Brown, McFadzean, Purver, Harvey, Crookes, Roberts, Liburd (Correia 64), Odejayi (Fondop 45). Unused substitutes: Rooney, Correia, Lenighan, Fondop, Niate
Referee: Ryan Johnson.