Miller's hopeful inswinging cross from the left deceived visiting goalkeeper Steven Collis to give the home side a share of the spoils in a clash the visitors dominated.
With both sides having suffered successive League defeats, a return to form was imperative over the busy Christmas period.
After Miller had fired an effort inches wide in the sixth minute, it became one-way traffic with Steve Tilson's men laying siege to the Gillingham goal, forcing a succession of chances that should have resulted in a goal.
Leon Clarke was the chief culprit, failing to convert a goalmouth scramble on 11 minutes before heading over Tommy Black's pin-point cross from close range moments later.
And in the 24th minute Leon Clarke saw his eight-yard shot brilliantly parried by Simon Royce moments after the goalkeeper had denied Charlie MacDonald with another fine stop from point-blank range.
Gills manager Mark Stimson clearly needed to act and withdrew youngster Craig Stone for Barry Cogan in the 31st minute, reverting to a 4-4-2 formation in an attempt to stem the tide of Southend attacks.
But the change failed to alter the pattern of play and the Shrimpers finally got the goal their pressure deserved in the 54th minute from a regulation free-kick.
Steven Hammell's inswinging delivery found the unmarked Peter Clarke who glanced his header just inside Royce's far post.
The home side gradually increased the urgency of their play but Royce remained the busier keeper, palming away Mark Gower's 20-yard drive as the game entered the latter stages.
It appeared that Gillingham were heading for a third successive defeat until the ball reached Miller on the left and his cross missed everyone before sneaking in at the far corner.
Seven minutes of stoppage time ensued during which Gillingham's Stuart Thurgood saw red for a rash tackle on Kevin Maher, but neither side could grab a winner.