The Railwaymen appeared to be heading for defeat as they trailed 3-1 with just over 20 minutes to go, but the introduction of Rodney Jack sparked Crewe into life
The little West Indian cracked in a 25-yard belter with his right foot to give his side a fighting chance and set up a grandstand finish at Gresty Road.
Gillingham appeared to be coasting towards a comfortable win after a trio of stunning strikes in the first half from Alan Pouton, Michael Flynn and Dean McDonald put them in command.
After home striker Nicky Maynard had blazed over Pouton stepped up with a fierce half volley from 25 yards with flew into the top corner in the 20th minute.
Midfielder Flynn came up with almost as breathtaking a finish eight minutes later when he curled McDonald's lay-off into the far corner.
Crewe struggled to make an impression in the final third and Ryan Lowe, who had hit a hat-trick seven days previously, was way off the mark with a long-range volley. But he put Maynard through nine minutes before the interval and the youngster kept his composure this time to slot across Scott Flinders into the far corner to reduce the arrears.
But Gillingham restored their two-goal advantage after a searing run from Guylain Ndumbu-Nsungu down the right. He cut the ball back and McDonald swivelled on the edge of the six-yard box and fired high into the far corner.
Crewe, who had won their five previous home games, struggled to find inspiration in front of goal until Jack was introduced in the 63rd minute.
And soon Flinders was picking the ball out of the net. But it appeared the visitors had held on for a win when Julien Baudet lofted a juicy chance over from eight yards out after Jon Otsemobor's free-kick had deflected nicely into his path.
But they hadn't bargained for the spirit of the home side which drove them forward in the closing minutes and substitute Danny O'Donnell headed in at the near post from a Michael O'Connor corner.
Flinders did well to keep out O'Connor's piledriver in the four minutes of added time, but the keeper was helpless when his defence failed to deal with a lofted free-kick and Varney ghosted in at the far post to volley in a dramatic winner.