Chris Edwards' deflected free-kick 12 minutes from time helped Town stretch their unbeaten run to a club record nine games at Rede Court Road on Tuesday night.
Micky Collins' new-look side boasted another new signing in Greg Benbow, but the downside was having Adam Marsh and Keiron McCann both sent off.
Rochester also had defender Tom Carr dismissed for two yellow cards as the contest ended 10 v 9.
Marsh was the shown a straight red following a skirmish as Town celebrated following Chinedu McKenzie's 41st minute opener.
Carr fired the home side level on the hour, before being booked twice in the space of four minutes, and McCann followed him for the same reason.
Town carved out several chances in the opening half hour, the game delayed for several minutes with home goalkeeper Roddy Hayward needing treatment for an injury to his right ankle.
McKenzie and Marsh twice, and Joe Bingham went close inside the opening 20 minutes.
Marsh then got on the end of Ben Bridle-Card's long kick downfield only to see his shot saved, before new-boy Stephen Okoh was denied by Hayward and a defender.
Town went in front four minutes before half-time, but it came at a cost.
McKenzie finished well as the ball came in from the left, his first goal for the club, but the joy was cut short when Marsh was shown a straight red card.
Bingham and McCann also picked up yellow cards first half bookings, which was to prove costly for the latter.
Carr made it 1-1 beating Bridle-Card with a left foot finish from the edge of the box.
He was then booked for giving away the free-kick which led to Edwards match-winner, his 20-yard effort getting a touch inside the box before hitting the roof of the net.
Six minutes later Carr was sent off for his second foul, before McCann picked up his second yellow, and follow him to the dressing room.
Benbow made his debut as a 73rd minute substitute - an experienced attacking left-sided midfielder who has had spells with Chatham and VCD in the past.