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Cody McDonald rescued a point for the Gills with a stoppage time equaliser.
Gillingham had been on course for a second defeat in four days, having conceded in the 90 minute with the scores at 1-1, just as they had on Boxing Day against Leyton Orient.
But McDonald, who scored a stunning opener early in the second half, fired home to level the game at Priestfield.
Gills boss Peter Taylor made three changes to the team which lost 2-1 at Priestfield on Boxing Day, with Charlie Lee, Bradley Dack and Adebayo Akinfenwa all dropping to the bench.
Making a surprise start for the Gills was Danny Kedwell, less than a week before going in for a hernia operation. Whelpdale and Craig Fagan also came in for the Taylor’s side.
Kedwell was to end up playing the full 90 minutes.
The first half was dominated by the visitors, who had the majority of the possession. But despite that the best chance of the half fell to the Gills.
A rare Gills attack saw McDonald leave defender Andy Butler on his backside, but Kedwell was unable to convert the cross, as he slid in at the far post.
Walsall, for all of their possession, were unable to find a way through, with Romaine Sawyers hitting a low shot at goal that keeper Stuart Nelson used his feet to save.
Ashley Hemmings, with a header and a shot, went wide twice while Craig Westcarr also put an effort the wrong side of the post.
The first half had failed to excite and referee Trevor Kettle kindly blew for the break without an extra time being added.
If the opening half had been dull, the second burst into life, as McDonald beat keeper Richard O’Donnell with a super overhead kick from the edge of the box – just 21 seconds after the restart.
O’Donnell made a great block from McDonald moments later, to deny the Gills striker his second, but had the crossbar to thank when he was beaten by Whelpdale as he lobbed the loose ball towards goal.
Walsall were back on level terms just past the hour. Sawyers initial effort from James Baxendale’s cross was cleared off the line by Leon Legge and the ball fell invitingly for the visiting forward to bury into the net, infront of a jubilant 168 travelling fans.
The visitors should have taken the lead 10 minutes later, when Nelson spilled a powerful Sam Mantom effort into the path of Sawyers. The Walsall player took the ball past the Gills keeper but from an angle he fired wide.
The Gills conceded just 30 seconds before the 90 minutes were up, as Julian Gray tucked the ball home for Walsall.
But the game ended all-square when McDonald scored his and Gills second infront of the Rainham End. The visiting defence had stopped, when McDonald at first went down under a challenge, but the Gills number 10 got to his feet and tucked the ball home.
McDonald could even have won it for the Gills, with a chance at the death, but keeper O'Donnell pulled off a good save to deny him the hat-trick.
Gillingham: Nelson, Harriman, Martin, Barrett, Legge, Hessenthaler (Davies 74mins), Fagan (Akinfenwa 74mins), Gregory, Whelpdale (Lee 82mins), Kedwell, McDonald. Subs: Howard, Dack, German, Daniels.
Walsall: O’Donnell, Purkiss, Taylor, Butler, Chambers, Mantom, Hemmings (Gray 85mins), Downing, Baxendale (McQuilkin 88mins), Sawyers, Westcarr. Subs: Featherstone, Benning, Chambers, Hewitt, Lewis.
Attendance: 5,394