Antonio German and Chris Whelpdale put the Gills two goals to the good before Jason Banton pulled one back for Argyle.
Second-placed Port Vale saw their recent slump continue as they were beaten 2-1 at home by play-off chasing Southend.
Sean Clohessy put Southend ahead from the spot and Britt Assombalonga doubled their lead, meaning Lee Hughes' goal was not enough for Vale, who have lost four of their last six matches.
Robbie Weir struck twice as Burton went third by beating fifth-placed Cheltenham 3-1. Alex MacDonald got Albion's other goal with Byron Harrison netting a late consolation for their opponents.
Torquay slipped closer to the relegation zone as they went down 3-1 at home to Oxford.
James Constable and a Damian Batt penalty put the visitors 2-0 up. Aaron Downes gave Torquay hope but Simon Heslop's late strike sealed the win.
Accrington could not take advantage of Torquay's defeat as goals from Chris Hackett and Roy O'Donovan saw them beaten 2-0 at fourth-placed Northampton.
Ten-man Rotherham slipped to sixth after a 2-1 defeat at home to Dagenham and Redbridge.
The home side had Kari Arnason sent off after bringing down Medy Elito in the area, and the Congolese midfielder picked himself up to open the scoring from the penalty spot.
Claude Davis pulled the Millers level but Luke Wilkinson grabbed the winner eight minutes from time.
George Donnelly's late double helped Rochdale to a 4-1 win over Wycombe.
Stuart Lewis had put Wanderers' ahead but an Ian Henderson strike and Michael Harriman's own goal saw the home side hit back before Donnelly sealed the win.
Fleetwood and Exeter played out a goalless draw while James O'Shea and Armand Gnanduillet gave Chesterfield a 2-0 success over Bristol Rovers.
Substitute Alan Connell scored a last-gasp penalty to earn Bradford a 1-1 draw against Aldershot, Kieron Cadogan had put the visitors ahead at the end of the first half.
Barnet hammered 10-man Morecambe 4-1 thanks to a Daniel Lopez hat-trick after the visitors had goalkeeper Barry Roche sent off.
Jack Redshaw put Morecambe ahead but Luke Gambin levelled and Lopez's first made it 2-1.
Roche then brought down Gambin in the area and saw red, with Lopez converting the resulting penalty before completing his treble to improve the home side's survival prospects.
Wimbledon hauled themselves out of the relegation zone as they emerged 3-2 winners over York, condemning visiting manager Nigel Worthington to a losing start.
Mat Mitchel-King put the Dons ahead but Chris Smith quickly headed in an equaliser.
Brennan Dickenson put Wimbledon back ahead, only for Smith to level for a second time. But Harry Pell got the clinching goal with 11 minutes remaining.
