Signed from Millwall on Monday as cover for the injured Marc Richards, Marquis continued where he left off in his previous spell with the club, sealing victory at York City with the crucial second goal of the evening to send Town further clear at the top of the table.
James Collins had broken the deadlock at Bootham Crescent, five minutes before half-time, as Northampton completed the double over the Minstermen in the space of less than a month despite a late consolation goal from Russell Penn for the home side.
With Plymouth being held at Yeovil, Chris Wilder's side are now twelve points clear in League Two and, speaking to the official club website after the game, the Town manager said: “We mixed the team up a bit tonight and I thought John Marquis was outstanding.
"John-Joe O’Toole has a bit of a tight thigh but Jason Taylor came in and he can be delighted with his efforts."