Novak steered in the rebound from close range on 76 minutes after substitute Anton Robinson hit a post with a scuffed shot. Town, now unbeaten in 37 league matches, nearly made a mess of it, though, with a disjointed second-half display.
And Stevenage were handed a golden opportunity to equalise for a second time in the 90th minute, but John Mousinho blazed a dubious-looking penalty over the crossbar after Antony Kay was punished for an innocuous challenge on Byron Harrison.
Boro boss Graham Westley's touchline antics throughout the match sparked a brawl at the end involving opposite number Lee Clark. Players from both sides squared up in an ugly melee that took several minutes to die down after the final whistle.
Stevenage, trailing to a Gary Roberts strike after 44 minutes, almost levelled when Mousinho had a shot cleared off the line by Calum Woods.
The visitors were outplayed in the first half but looked a different side after the break, and their pressure finally told when Mousinho set up Scott Laird, who unleashed an unstoppable low drive in off the post after 67 minutes.