The Heed took the lead through Sam Carson but were pegged back on the stroke of half time by a goal from Will Jenkins.
Quickfire strikes from Sam Hodgson and Ben Errington put the Mariners two goals ahead, and although Kieron Clark halved the deficit it proved insufficient to rescue the tie for the hosts.
South Shields began the evening on the front foot, striking the crossbar twice within the opening six minutes through a Joe Lockey shot and a Will Morris cross.
Gateshead goalkeeper Alfie Gordan was forced to make a smart save from close range shortly afterwards to prevent Joao Gomes from opening the scoring with the hosts penned back early on.
The Heed grew into proceedings the further the half wore on however, seeing their first shots on target midway through the opening period as Charlie Hindson’s 20-yard effort was kept out by Shields ‘keeper Aaron Steavans.
Carson put the hosts in front with half an hour gone, finding space on the edge of the box before sending a powerful left-footed strike in off the post to leave Steavans helpless.
Jenkins cancelled the opener out on the stroke of half time however, rounding off a well-worked Shields move to place Morris’ cross into the bottom corner and level the tie up.
A quickfire double saw the Heed fall two goals behind within nine minutes of the restart and set them on the back foot before they could regroup however.
Josh Croft slipped Sam Hodgson inside the box and the forward finished into the far corner to put the Mariners in front, three minutes before his 20-yard shot was flicked into the back of the net by Errington to make it three.
Gateshead’s heads didn’t drop despite the setback, and they hauled themselves back into the game two minutes after falling two behind as Clark robbed Steavans of possession on the edge of the box before promptly tapping into an unguarded net.
The final half an hour of the tie proved to be hotly contested with Tom Green hitting the side netting for Shields while Kieran Adamson forced Steavans into a save as the Heed chased the game.
A third goal proved to be a step too far for Gary Middleton’s side unfortunately, and they were forced to accept defeat and an FA Youth Cup exit at the preliminary stage.
Gateshead XI: Gordan; Bolton, Evans, Carr, Patterson, Jackson, Thomas (Adamson, 75’), Leech, Clark (Leveney, 86’), Carson, Hindson.
Unused subs: Turoski, Doxford, Ede, Lawrence, Thebe.
Goals: Carson (30’), Clark (56’)
South Shields XI: Steavans, Wade, Croft, Ames (Dunn, 65’), Errington, Lockey, Morris, Black,S. Hodgson, Jenkins (Green, 65’), Gomes.
Unused subs: E. Hodgson, Williamson, Taylor.
Goals: Jenkins (45’), Hodgson (51’), Errington (54’)
Bookings: Lockey (10’)
Referee: Daniel Van Hymus