Bolton graciously gave their hosts a guard of honour as the teams came out, but their respect almost extended to giving the Welsh club the lead after just 34 seconds.
Craig Conway was afford acres of room down the right and when his ball eventually broke to Jordon Mutch just six yards out he looked certain to score, but Adam Bogdan made an outstanding save low to his right.
The champions bossed the early exchanges and almost took a fortuitous lead when Kim Bo-kyung's cross struck Lee Chung-yong and flew narrowly wide of Bogdan's near post.
But it was the visitors who grabbed the opening goal against the run of play.
Sam Ricketts skipped past Conway down the Bolton right and his pull-back was emphatically driven home by Eagles.
Cardiff huffed and puffed in search of an equaliser, but the Trotters were visibly more assured after their goal, and should have doubled their advantage just past the half-hour mark.
Eagles, featuring increasingly prominently, surged away down the left and teed up Darren Pratley at the far post, but David Marshall was out quickly to deny the former Swansea midfielder.
After a frustrating first 45 minutes Cardiff piled on the pressure upon the resumption, although they were struggling to find an end product.
Mackay decided to introduce Tommy Smith and Noone off the bench, and the former should have had Cardiff level in the 65th minute.
Noone rolled a well-weighted pass across the face of goal to find Smith unmarked just six yards from goal, only for Bogdan to scramble heroically and make the save.
But the Hungarian was finally beaten just three minutes later, Noone stepping up to curl a free-kick inside his near post.
The final quarter was all Cardiff as they looked to mark their title party with a victory, and Gestede headed a good chance straight at Bogdan.
Bolton almost snatched a crucial victory when Ben Turner's back pass sold Marshall short, but the keeper did enough to prevent Pratley from pouncing.