An incredible finish saw Wanderers take the win in their second Central League Cup fixture.
All the talking points were delivered in the second half with the crowd at Lostock witnessing an especially cagey first half.
Dubem Eze had the first real chance of the game on 23 minutes but an unfortunate slip saw his effort from the edge of the area roll wide.
Noah Halford captained the side in a more deeper role than usual and the midfielder almost opened the scoring as he met a swinging corner with his head but the ball dropped just wide three minutes later.
Despite these chances for Wanderers it was the visitors who took the lead five minutes into the second half from the penalty spot which looked an incredibly harsh decision from referee Daniel McDonald.
Robbie Clearly stepped up and scored to put Salford up 1-0 with 40 minutes still to play.
Just two minutes after the deadlock had been broken Wanderers went up the other end and rattled the frame of the goal.
Mark Isong was picked out by a Eze cutback with the forward swinging his left leg at the ball but it cannoned against the bar and went out of play.
The captain was in the action once more as a Wanderers attack was initially cleared only as far as Halford but he simply put too much on it as it went over the bar.
Controversy with 15 minutes to go as substitute Trevon Bryan seemed to have equalised for the Whites with a thunderous strike hitting the underside the the crossbar and going over the line.
However Daniel McDonald waved play on and ignored the Wanderers protests. With the ball crossing the line before hitting the stantion and bouncing back into play, the man in the middle believed the ball must have hit the post. So the game remained 1-0.
Sonny Sharples tried his luck on 80 minutes following a cleared corner but once again the effort went over the bar and didn't trouble James Carr in the Salford goal.
Ajay Weston got in behind the Salford defence on the left and put the ball on a plate for Conor Lewis at the back post but a remarkable save from Carr continued to frustrate Wanderers.
Finally the goal came on 90 minutes when defender Sean Hogan picked out Luke Matheson in the opposing half who dinked the ball over Carr to ensure the Whites wouldn't leave Lostock empty handed.
But the goals kept coming, substitute David Amimbola gave Wanderers the lead in the third minute of stoppage time after a quality ball was delivered across the face of goal for the forward to tap home.
The win was sealed at 90+7 when Bryan weaved his way into the Salford area and at the second attempt got his deserved goal and a much earned win for Wanderers.
Wanderers: Dallimore, Westwood (52' Smith), Matheson, Hogan, Grayson (68' Lewis), Weston, Sharples, Halford, Eze, Fleury (52' Bryan), Isong (80' Amimbola)
Subsitutes: Irwin
Salford City: Carr, Lancaster, Lara, Ogara, Collins (55' Heys), Hamman, Henderson (80' Bairstow), Davies, Malcolm, Clearly, Da Costa (80' Butt)
Substitutes: Midgley, Bowen