Dan Sweeney's 89th minute header dealt a cruel defeat to Harrogate Town who had looked set to end a run of nine straight Boro victories at Lamex Stadium.
Stevenage had time and time again been denied by the visitors, with Pete Jameson on impressive form between the sticks, but Sweeney was able to glance home in the dying seconds to send Harrogate home empty handed.
Simon Weaver made three changes from last weekend's draw at Stockport County as Rory McArdle, Matty Daly and Jack Muldoon replaced Miles Welch-Hayes, Stephen Dooley and Sam Folarin.
Daly nearly marked his return to the starting line-up by opening the scoring inside the first minute, but his first time left footed effort whistled wide.
Town's best chance came in the seventh minute when a high press resulted in Josh Coley gaining possession, dribbling past a defender and finiding himself one-on-one with Taye Ashby-Hammond, who extended an arm to deny the chipped finish.
Jameson then made the first of a string of impressive first half saves in the 17th minute, standing tall until the last minute to block Alex Gibley's effort.
Kayne Ramsay and Coley were combining well down Town's right hand side and almost created an opportunity for Luke Armstrong to head home, but it was the hosts who would finish the half the stronger.
After Luke Norris had glanced a header wide, Jameson made an impressive double save to keep out Danny Rose's header and Jake Taylor's follow up to ensure the score remained goalless at the break.
Jameson was back in action five minutes after the restart, this time making a more straightforward save from Taylor's header.
Norris had a good chance to open the scoring in the 54th minute after another good Kane Smith delivery, but the lack of chances created was clearly frustrating Boro boss Steve Evans, who opted for four changes just after the hour mark.
One of those four changes was Jamie Reid, who nearly produced the opener not long after his introduction, turning sharply before seeing his shot deflect behind.
The crossbar then denied Stevenage the lead as Rose's cross to the back post bounced off the upright onto Alex Pattison, then back onto the bar before Jameson could punch clear.
With just a minute left of normal time, Town hearts were again broken with a late goal for the second time in three games, Sweeney heading home a deep Gilbey cross into the box to secure a tenth successive home victory for his side.
Town: Jameson, Mattock, Burrell, Coley (Folarin 69), Richards, Pattison, Muldoon (Angus 75), Ramsay, McArdle, Daly, Armstrong
Subs not used: Oxley, Welch-Hayes, Headley, Austerfield, Dooley
Stevenage: Ashby-Hammond, Clark (Earley 62), Piergianni, Sweeney, Taylor (Roberts 62), Norris (Reid 62), Campbell (Reeves 62), K Smith, Vancooten, Gilbey, Rose
Subs not used: Chapman, Read, Bostwick
Goal: Sweeney 89
Referee: Sam Allison
Attendance: 2,547 (75 away)