Josh Poole squeezed the ball home in the 93rd minute after the Yellows had failed to clear a corner to cancel out Dylan Vassallo’s first half strike.
It was an opportunity missed for the Yellows, who had looked set to close the gap on the league leaders and take advantage of teams dropping points around them.
As it was, in just their seventh league game in three months, the Yellows had to settle for a point which may have a come at a cost, with captain James McCarten forced off in the second half with a foot injury.
These two were meeting for the fourth time this season, having met recently in the FA Trophy and drawn 0-0 in the reverse league fixture at Cantilever Park.
On a rough pitch, the game started in lively fashion with Jamie McDonald going close with what would have been a goal of the season contender, a sublime volley from Tony Gray’s lofted through ball.
At the other end, Jordan Hulme latched on to Poole’s reverse ball and forced a smart stop from Tony McMillan.
But it was Warrington who would break the deadlock on 18 minutes, Gerard Kinsella’s cross headed out to Vassallo, and while he didn’t hit it well, it would fade away from the ‘keeper in almost slow motion and find the corner.
Altrincham were very fortunate to keep their full complement of players on 23 minutes when the already booked Simon Richman hacked down Vassallo on half way as the Yellows launched a counter attack.
That would trigger a niggly remainder of the first half where the referee was kept busy with plenty of cards dished out.
There were four yellows handed out before half time, which saw Richman dragged off for Altrincham as well as McDonald, both on yellow cards.
Altrincham started the second half well and forced a smart stop from McMillan off Connor Hampson’s shot, before the yellow card was out again when Shaun Densmore wiped out Gray, who hobbled on to continue but would eventually be forced off with his knock.
Vassallo got his name in the referee’s notebook before McCarten did likewise on the hour mark, with a challenge that would force him off injured, with early suspicions he may have broken a bone in his foot.
With their captain and backbone of the defence off the field, the Yellows dropped deep and the last 10 minutes they would be clinging on.
And just as it looked like they had done enough, Altrincham gained revenge for the late show Warrington handed to them in the FA Trophy replay.
Will Hayhurst failed to clear a corner and as the ball was played back across, Poole got just enough on it to fire the ball over the line, despite the best efforts of Adam Carden and McMillan.
It will have felt like a defeat for the Yellows, who must now dust themselves off for a Cheshire Senior Cup tie at Winsford on Monday before the FA Trophy clash at Wealdstone next Saturday.
Altrincham: Thompson, Densmore, Hampson, Jones, Harrison, Moult (Peers), Johnston (Miller), Richman (Harrop), Hulme, Poole, Hancock. Unused subs: White, Sheridan.
Warrington Town: McMillan, Carden, McKeown, Williams, McCarten (Higgins), Goulding, Kinsella, Vassallo, McDonald (Milne), Gray (Beeley), Hayhurst. Unused subs: Ascroft, Barnes.