McDonald, a half-time replacement for Guylain Ndumbu-Nsungu, headed home from close range to ease the home side's relegation fears.
City, who had won their previous five away outings in League One, began strongly and carved out an early opening on 11 minutes, when Enoch Showunmi turned his man and fed Brian Wilson, only for the winger to blaze his effort well over.
Gillingham's play rapidly improved thereafter and, on 27 minutes, Ben Chorley's goalbound header required a goal-line clearance after Ian Cox diverted Nicky Southall's free-kick into his path.
Moments later, it was Cox's turn to perform the goal-line heroics, clearing a Showunmi header away from danger as the Robins searched for the opener.
But a minute before the interval, the Gills wasted arguably the best chance of the half when Danny Spiller cut inside following Andrew Crofts' through ball but saw his shot deflected over.
Gills manager Ronnie Jepson introduced McDonald at half-time and the move proved inspirational.
After narrowly failing to hit the net on 54 minutes, McDonald made no mistake a minute later, defying his lack of height to head home Mark Bentley's cross at the far post.
The Robins poured forward and, in the 79th minute, came desperately close to an equaliser when Gillingham's Clint Easton and Robins substitute Jennison Myrie-Williams contrived to head against the crossbar, before Lee Johnson fired over.
Minutes later, both Spiller and Showunmi missed decent opportunities for their respective sides and, with a minute remaining, Johnson danced through the Gillingham defence only to be denied by a last-ditch tackle by Chorley.
It proved to be the final chance of note for Gary Johnson's men, who were unable to turn their late pressure into an equaliser.