Nine players were booked and several were on last warnings, but the home side did just about enough to take the points.
Adam Miller and Jackson put them 2-0 up at the break, but Jack Lester pulled one back and was only denied a second by an outstanding save from Simon Royce.
Both Gillingham and Chesterfield were three days away from important second round FA Cup ties, with attractive fixtures against Aston Villa and Ipswich awaiting respectively in the third round.
A bright opening banished any fears the players would be distracted, with Lester almost scoring on 12 minutes with a curling shot that brushed the outside of the upright.
Somewhat against the run of play, Miller gave Gills the lead from close range after excellent work down the left from Andy Barcham.
Jamie Ward and Jamie Lowry had already made their way into the referee's notebook when the game took on a nasty atmosphere after 30 minutes.
Mark Bentley and Rob Page squared up to each other and were both booked.
The frequent interruptions disrupted the game, but in stoppage time Jackson provided the one moment of genuine quality.
Miller flicked on a long ball and Gills' top-scorer lobbed Trevor Carson for his ninth goal of the season.
The hosts looked uncertain as to whether push on or defend their lead after the break and Lester took advantage of the uncertainty when he converted Darren Currie's cut back on 60 minutes to haul the visitors back into the game.
The procession of bookings continued as the contest fragmented.
Lester had the best chance to snatch a point for the Spireites on 78 minutes but his sweetly-struck effort was brilliantly stopped by Royce low to his left.