Paddy Lane and Charlie Kelman were both sent off for going into a 50-50 challenge dangerously, with the Fleetwood man stretchered off with a potentially serious injury.
The stalemate leaves Fleetwood still a one point shy of safety behind Neil Harris’ Gills, but still three points ahead of AFC Wimbledon after they drew 1-1 at home to Wycombe Wanderers.
The Cod Army host the Dons on Saturday in a huge relegation six-pointer.
Stephen Crainey made two changes from Good Friday’s 3-2 defeat at home to Oxford as Alex Cairns reclaimed his place in goal following suspension and Josh Harrop came into the front three as defender Tom Clarke stepped down.
It signalled a tactical switch for the Cod Army as Zak Jules moved to left-back in a back four, with Harvey Macadam taking up the other full-back slot.
Gillingham, themselves fighting at the bottom of the table, started the day one point and one place above Fleetwood, but crucially outside of the relegation zone.
After seeing off Crewe 3-1 in their last away outing, Fleetwood started brightly, with Ellis Harrison’s speculative volley finding the side-netting before a pair of dangerous Macadam crosses narrowly evaded firstly Harrop and then Harrison.
The returning Cairns was called into action for the first time on 34 minutes, when Ben Thompson sprayed the ball out to former Fleetwood man Ryan Jackson, whose cross picked out Kelman unmarked in the six-yard box.
However, the striker’s downward header was straight at the Cods keeper, who prevented the Gills opening the scoring in front of their largest home crowd of the season.
Cairns was in the action again two minutes later, after Kelman was played through, and the 29-year-old was out quickly to prevent the Gillingham frontman from getting a shot on goal.
Kelman then set up Thompson and the midfielder’s effort was gathered comfortably by Cairns before Callum Camps came closest for Fleetwood before the break, when his curling effort from distance was deflected narrowly wide.
Harrison was picked out by Dan Batty’s free-kick but his header was comfortably saved by Aaron Chapman in the Gills goal before Harrop’s shot was blocked by Max Ehmer.
The game’s controversial moment came on 78 minutes as Lane and Kelman both went after a loose ball, which neither won but the pair clashed and stayed down injured.
Kelman was given his marching orders once back on his feet and the 21-year-old Lane, who had to be stretchered off, also saw red.
The hosts piled on the pressure in the second half, with 10 shots on Cairns’ goal, but Fleetwood stood firm and secured their eighth draw away from home this season.
Gillingham: Chapman, Masterson (Phillips 90), Ehmer, Tucker; Jackson, O’Keefe (Reeves 46), Thompson, Lee, McKenzie (Tutonda 71)); Oliver, Kelman; Subs not used: Dahlberg, Maghoma, Chambers, Dickson-Peters
Fleetwood: Cairns, Macadam, Nsiala, Johnson, Jules; Hayes, Batty (Boyle 90), Camps; Lane, Harrison, Harrop (Pilkington 75); Subs not used: O’Hara, Bird, Baggley, Garner, Butterworth
Referee: James Linnington. Attendance: 8,436