The Birmingham loanee struck with a left-foot shot in the eighth minute of added time to take Jimmy Floyd Hasselbaink’s side two points clear at the top of Sky Bet League Two.
Burton looked doomed when full-back Damien McCrory’s penalty was saved three minutes into stoppage time, but Johnstone pounced on a loose ball in a goalmouth scramble to extend the hosts’ unbeaten run to nine games.
Skipper Danny Grainger stunned the hosts by giving Carlisle a second-minute lead with a terrific 25-yard free-kick.
United rode their luck as Burton piled forward in search of the equaliser. Grainger’s goalline clearance denied Tom Naylor and keeper Mark Gillespie kept out Stuart Beavon’s close-range shot before a McCrory effort hit the woodwork.
The visitors were under siege again after the break and Gillespie brilliantly got his fingertips to McCrory’s 18-yard free-kick.
And the Carlisle keeper surpassed himself with his penalty save after Beavon had been upended – only for Johnstone to have the final say.