Stevenage were left empty-handed after conceding an 82nd-minute winner to Carlisle at the Lamex Stadium on Saturday.
Caretaker manager Mark Sampson made four changes to the starting line-up from the previous weekend, following the departure of Dino Maamria.
And the home side had an early chance with only four minutes gone as Chris Stokes crossed for Craig Mackail-Smith, who knocked the ball down to Danny Newton to fire straight at visiting keeper Adam Collin.
Carlisle's first effort at goal came on 21 minutes when Harry McKirdy tried an audacious chip over Paul Farman, but saw the ball saileed over the bar and onto the roof of the net.
And Boro broke the deadlock three minutes later when Kurtis Guthrie sent a half volley from just inside the box into the bottom left corner of the net, before running towards the interim management celebrate.
Newton shot straight at Collin on 27 minutes, but Carlisle had two chances in quick succession as Olufela Olomola and Jack Iredale were denied by last-ditch defending.
And the visitors were back on level terms on 37 minutes as McKirdy beat the offside trap and fired past Farman.
Ben Kennedy had two late chances for Boro, but fired a free-kick into the defensive wall and then shot over from Newton's pass outside the box as the first half ended all square.
Carlisle went close after the restart as Olomola headed wide at the far post on 47 minutes and they took the lead soon after through Nathan Thomas.
But their joy was shortlived as Guthrie claimed his second goal of the game, heading over the keeper at the far post after a fantastic cross by Stokes.
Tyler Denton replaced Luis Fernandez in the first change of the day and put in a cross to the back post for Guthrie, who put it straight at Collin.
Kelland Watts did well to take the edge off a shot from Olomola, allowing Farman to collect, before Elliott List replaced Mackail-Smith.
And List went close to putting Boro ahead after running on to Kennedy's pass and rounding the keeper, only to see his tight-angled effort cleared off the line.
Carlisle went 3-2 up with only eight minutes left, though, as McKirdy's deflected effort found the net and Boro could not get back on terms despite five minutes of stoppage time.
Stevenage: Farman, James-Wildin, Stokes, Carter, Kennedy, Husin (Cowley 85), Newton, Watts, Guthrie, Fernandez (Denton 56), Mackail-Smith (List 65).
Unused subs: Bastien, Iontton, Taylor, El-Abd.
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