Chasers Port Vale and Cheltenham both slipped up as the gap to the Gills increased to seven points. Daniel Nardiello grabbed a double for Rotherham to sink the Robins, while York held Port Vale to a 2-2 draw.
At the other end of the table, Adebayo Akinfenwa's rich vein of scoring form ensured that Wycombe remain rooted to the bottom.
Southend also recorded a fine 4-1 result at Torquay thanks to three first-half goals and Chesterfield struck late to beat Oxford United 2-1.
Results in full: AFC Wimbledon 1-1 Aldershot, Bradford 0-1 Exeter, Burton Albion 3-2 Dagenham & Redbridge, Chesterfield 2-1 Oxford United, Fleetwood 3-0 Plymouth, Gillingham 2-1 Morecambe, Northampton 3-1 Wycombe, Port Vale 2-2 York, Rochdale 2-1 Bristol Rovers, Rotherham 4-2 Cheltenham, Torquay 1-4 Southend