The Scotland international opened the scoring with a fine strike from the edge of the area and then scored a stunning over-head kick from inside the area in the second half at Turf Moor.
Gordon Greer's late header earned a deserved three points for the Seagulls, who are now unbeaten in their last three games, and going well in their second season back in the npower Championship.
For Burnley, who had levelled through Greer's own-goal after 60 minutes, it was a third game without a win and after a tame attacking display, a big improvement is needed if they are to challenge this season.
Brighton boss Gus Poyet was one of the busiest on transfer deadline day, bringing in four players, but none of them made his starting XI, with the inclusion of Kazenga LuaLua the only change from last week's 5-1 thumping of Barnsley.
It was a quiet opening to the game with neither side hitting their straps early and the only moment of drama in the opening 15 minutes was when Kieran Tripper went down with a nasty looking injury.
The England Under-21 international was fine to carry on, though, and he watched his side fall behind as the visitors opened the scoring with the first shot on goal in the 18th minute.
Gary Dicker pinged a free-kick to Mackail-Smith and the prolific striker, who was linked with a move to Norwich this week, fizzed in a fine 20-yard effort for his third goal of the season.
Unfortunately that did not spark the game into much life. The goalkeepers were not enduring a busy time and LuaLua fired an effort well wide as there was little goalmouth action of note.
Burnley boss Eddie Howe introduced Martin Paterson in place of Marvin Bartley as he tried to improve his side's attacking prowess after the break, but it was Brighton that nearly doubled their advantage when Ashley Barnes had his header saved by Lee Grant.
Brighton were enjoying their most incisive spell and LuaLua made light work of Trippier, but his shot went just wide, grazing Grant's post.
But that seemed to spur the hosts into action and they had their first meaningful effort on goal when Charlie Austin headed Trippier's cross onto the roof of the net.
The Clarets were not to be denied, though, and they levelled on the hour when the visitors could not deal with a vicious Junior Stanislas cross and it skimmed off Greer's head and into the corner.
And they should have taken the lead a couple of minutes later when Stanislas was in the thick of the action again, but he put his header from Ross Wallace's cross wide when he should have scored.
Burnley were in a fine spell and Wallace powered in an effort from 35 yards that former Manchester United goalkeeper Tomasz Kuszczak did superbly to divert over the goal.
But Brighton hit back and took the lead with a goal of the highest quality through Mackail-Smith, who had been denied moments earlier by a fine Grant stop.
The Burnley keeper was helpless to the striker's next effort, though, as he found the corner with an outstanding over-head kick in the 77th minute.
The points were wrapped up in the 87th minute when Andrea Orlandi's cross was headed home by Greer, who made up for his earlier misdemeanour.