Leon Legge's goal on the half-hour gave the Gills the advantage but that was cancelled out by Femi Ilesanmi seven minutes into the second half.
A 69th-minute penalty from Deon Burton put Gillingham back in front, though, and they defended that lead to move two points clear at the top.
Port Vale slipped to second with a 1-0 loss at home to Morecambe, courtesy of Lewis Alessandra's 64th-minute goal. Morecambe played the last 17 minutes with a man less after a red card for Andrew Wright but Vale were unable to find the target.
Burton moved into the automatic promotion places with a 4-0 hammering of play-off chasing Fleetwood. Jacques Maghoma scored twice for the visitors, the first from the penalty spot, with Billy Kee and Calvin Zola adding to the tally in a dominant second-half performance from Albion.
That pushed Cheltenham out of the top three, with the Robins held to a 1-1 draw by relegation-threatened Aldershot. Danny Rose gave the visitors a surprise 24th-minute lead but Paul Benson levelled things up midway through the second half, before Anthony Tonkin was sent off for the Shots.
Rotherham and Northampton gave their play-off hopes a boost with wins. The Millers edged past Chesterfield 1-0 with a second-half goal from Johnny Mullins, while the Cobblers had Kelvin Langmead to thank for their 2-1 win at Southend.
Wimbledon remain at the foot of the table but moved within a point of safety with a late 2-1 win over Capital One Cup finalists Bradford. The Yorkshire club led through Garry Thompson, but Jack Midson evened things up seven minutes from time before Gary Alexander hit a last-minute winner for Wimbledon.
Ryan Brunt scored the only goal as Bristol Rovers beat Wycombe 1-0, and it was the same scoreline at the Spotland Stadium where Rochdale saw off Torquay with a first-half effort from Rhys Bennett.
James Constable was on target for Oxford United in a 1-0 victory at Plymouth, while Barnet came from behind to claim a 2-1 win at York with goals from Andrew Yiadom and Jake Hyde. Michael Rankine had put York ahead after seven minutes at Bootham Crescent.
- Sports & Recreation
- Deon Burton
- Lewis Alessandra