Jason Kennedy bundled in to give the visitors a 15th minute lead only for Matty Godden's penalty to level things up right on half-time.
Boro battled away and created numerous half-chances but Danny Grainger scored the winner from the spot 10 minutes after the break to give the Cumbrians all three points.
Darren Sarll named an unchanged XI from last weekend’s win at Morecambe. The only changes came on the bench where Harry McKirdy and Dean Wells replaced Rowan Liburd and Jake Hyde.
The game started in lively fashion as both teams looked to seek an early advantage, but it was the visitors who struck first on the quarter hour. Jamie Jones made two outstanding saves from point-blank range but was helpless as Jason Kennedy bundled the ball home from yards out.
Stevenage continued to push and enjoyed plenty of the ball in the first half but the visitors were showing why they have enjoyed an impressive start to the season and snuffed out any chances.
Darren Sarll’s men did manage to win a couple of corners as the half progressed and it was from a 42nd minute set piece that Boro drew level. Carlisle failed to really clear Henry Cowans’ cross and when Charlie Lee gathered possession and looked to dart into space in the box, the referee spotted a shirt-pull and awarded a penalty. Up-stepped Matty Godden and he gave Mark Gillespie no chance with a fierce finish for 1-1.
The striker then went close to a second right on half-time, latching onto a Gorman flick and turning in the box, but Gillespie saved his low shot.
Both teams came out unchanged for the second half and Jack King went close for Boro on 47 minutes with a header that was comfortable for the ‘keeper.
However despite coming out with renewed purpose, Stevenage fell behind 10 minutes after the break to another penalty. This time the referee deemed Luke Wilkinson to have climbed on his man and Danny Grainger made no mistake from the resulting spot-kick for 2-1.
Almost immediately Boro went close to equalising for a second time with two lovely balls into the Carlisle box defended away, with Henry Cowans then firing over from 18 yards just before the hour.
Darren Sarll threw on Harry McKirdy and Tom Pett for the final 20 minutes and both looked lively. On 72 minutes a good ball over the top from Ntlhe found McKirdy who took the ball to the byline and crossed, but King’s shot was blocked on the line.
Two minutes later Henry Cowans spread the ball out wide and Pett crossed for King to head at goal, but Boro’s attack was thwarted.
With 3 minutes left on the clock, sub Michael Tonge sprayed the ball out to Henry whose cross was met superbly by McKirdy, only for the Villa loanee to head straight at Gillespie.
Six minutes of added time were indicated and Boro pushed forward in earnest but just couldn’t find that telling through-ball or force that final chance to equalise.
Stevenage: Jones, Henry, Wilkinson, Franks, Ntlhe, Gorman (Pett 70), Lee, King, Cowans, Kennedy (McKirdy 70), Godden (Tonge 83)
Subs not used: Day, Fox, Schumacher, Wells
Carlisle: Gillespie, Grainger (Brisley 83), Joyce, Raynes, Kennedy, Jones, Wyke (Lambe 67), Adams, Gillesphey, Ibehre (Asamoah 84), Miller
Subs not used: Crocombe, Ellis, Devitt, McKee
Referee: Nicholas Kinseley
Attendance: 2,720 (447 away)