The hosts made heavy weather of it at times, hitting the woodwork three times as they fought to make the three points safe.
Carlisle got away to a blistering start with two goals inside the first 13 minutes from Rory Loy and a Lee Miller penalty as Stevenage went down to 10 men with the dismissal of goalkeeper Steve Arnold before Marcus Haber replied for Stevenage midway through the first half.
Loy, making his first home start in over 12 months after recovering from a broken leg, was on hand to steer a header past Arnold from Andy Welsh's cross to give Carlisle a ninth-minute advantage.
And it was Loy who was sent crashing inside the box by Arnold to win the penalty, which enabled Miller to drive the spot kick wide of replacement keeper Chris Day and double the lead four minutes later.
With Day on for the red-carded Arnold, Boro brought off striker Steve Beleck. But Stevenage pulled a goal back against the run of play in the 22nd minute when Haber got up well to meet Chris Gray's cross from the right and beat Mark Gillespie low down by the keeper's left-hand post.
There was nothing Day could do about a terrific Jon-Paul McGovern shot which shook the crossbar.
Carlisle failed to make their numerical advantage tell although substitute Dave Symington shuddered the bar with his first touch in the 77th minute, a 25-yard free-kick, then saw a shot from just inside the area hit the post.
Stevenage's best effort in the second half was a Luke Freeman shot, which had Gillespie stretching to save.