A stunning five-goal second quarter laid the platform for Mathew Buck's side in their 9.4 (58) to 6.8 (44) victory at Brighton Homes Arena on Sunday.
McKay (32 disposals, seven clearances), Mimi Hill (25, five) and Dayna Finn (29 touches, one goal) all shone for Carlton.
Bohanna kicked a game-high three goals, including two crucial majors in the final term to help seal the result.
It gave the Blues a 2-1 start to the season while the Lions - last year's beaten grand finalists - slipped to 1-2.
"It's just such a good feeling," former Gold Coast forward Bohanna told Fox Footy post-match.
"After the Hawks (loss) last week, we just knew if we stick to our process we can absolutely go with the best.
"That was what we did today and I just think the work rate of everyone was elite.
"We just stuck to the processes and we're just super, super happy."
Cartlon had eyes on an upset after kicking the first two goals against the run of play as Brisbane failed to make the most of their early dominance.
Buoyed by the bright start, the visitors ramped up their pressure and piled on five unanswered goals in the second term.
The best of them came from Keeley Sherar, who produced a brilliant right-foot snap when facing the boundary under pressure from three opponents.
Skipper McKay and fellow ball-winner Hill were superb in the first half and Erone Fitzpatrick kicked two majors, as the Blues led by 29 points at halftime.
Brisbane hit back hard and Ally Anderson (17 disposals, five clearances) lifted as the home side dominated the third quarter, kicking 3.3 to 0.1 to close within nine points.
But two Bohanna goals in the final quarter gave the Blues breathing space again and they held on for a stirring win.
Carlton can extend their positive start when they host the Western Bulldogs at Ikon Park in round four, while the Lions face a difficult interstate trip to take on Adelaide.
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