The Amex Stadium hosts had been unfortunate to have a second-half penalty appeal turned down, when Inigo Calderon tumbled over debut-making Sunderland goalkeeper Keiran Westwood, but Mackail-Smith ensured the newly-promoted Championship side went through to round three in any case on Tuesday night.
Defeat for Sunderland soured a week already forgettable for their fans following their 1-0 derby defeat to Newcastle at the weekend.
Sunderland boss Steve Bruce fielded a strong side with summer signings David Vaughan and Craig Gardner making their first starts alongside Westwood.
But despite the dangerous Stephane Sessegnon's early chance, when he drilled wide from a promising position in the third minute, it was Brighton who excelled with a slick passing style.
Ashley Barnes really should have given them a sixth-minute lead when, instead, he skied over the crossbar after Westwood failed to hold a long-range effort by £2.5 million signing Mackail-Smith.
There was also panic in the Black Cats ranks when Craig Noone's cross from the left sailed through a crowded goalmouth without attracting a decisive touch.
But Bruce's team, desperate to make amends for Saturday's derby defeat, gradually began to take control of the first half - without really looking like scoring.
Vaughan shot over after a promising run, cutting in from the right, and Gardner saw a shot blocked as did fellow new boy Sebastian Larsson with a tame header.
Their growing command of the opening 45 minutes counted for nothing, however, as Brighton turned the screw after the resumption.
Barnes again failed to finish when Noone's pass sent him scampering between two dithering defenders and soon afterwards, Calderon's perceptive pass put Mackail-Smith in the clear to slip the ball past the out-rushing Westwood only to see it bounce away off a post.
This time Brighton's siege lasted a lot longer, despite the loss of skipper Gordon Greer through injury at half time, when the diminutive Romain Vincelot - eventually carried off with a shoulder injury 14 minutes from time - had to replace him.
In the 64th minute, after Lewis Dunk and Noone had tested Westwood with headers, it looked like Brighton had won a certain spot-kick when the raiding Calderon tumbled over the goalkeeper after taking the ball around him in the box.
The boos were loud and inevitable after referee Andy D'Urso instead opted to book the Catalan for diving instead of pointing to the spot.
The setback could have destroyed the Seagulls but they kept battling and although goalkeeper Casper Ankergren made excellent saves to deny Sessegnon and Gardner, the Sunderland attack continued to look toothless for the rest of the 90 minutes.
It was the same story in the extra time but Mackail-Smith showed the way with his third Seagulls goal since moving from Peterborough in the summer.