The Bulls put in a vastly improved and outscored the Blues by three tries to two but the drop goal and two penalties from Nick Evans sealed the win.
Bulls fullback Zane Kirchner could have stolen the victory with five minutes to go but he lost control of the ball as he crossed the line.
Nick Evans proved six months too late he can land a match-winning drop goal.
The win lifted the Blues to second place with five wins from seven matches, while a third successive defeat on the road left the defending champions Bulls languishing near the bottom.
In a bruising encounter in which both sides revelled in fearless confrontation, the Bulls had the game in their grasp when they took a 21-20 lead with 15 minutes remaining.
But the Blues came back for Evans to land a drop goal in what became the deciding kick of the match.
A question that has vexed New Zealand since the All Blacks' 18-20 defeat in the World Cup quarter-finals last October was why Evans did not attempt a drop goal in the closing stages of that match. He did it in this match after all.
The reason given was that it was not a move the All Blacks had practised, but Evans showed for the Blues no rehearsal was necessary.
The Bulls had chances to equalise in the closing minutes when they won a series of free kicks inside the Blues 22 but were unable to work Derick Hougaard into a position to have his own drop goal attempt.
"I've lost like that before and it's not nice," said Blues captain Troy Flavell, who had reservations about the quality of his side's win.
In a fast-paced match where Springbok backrower Pierre Spies played the full 80 minutes in his first game since blood clots were found on his lungs last August, the Blues led 10-7 at halftime.
Flavell scored a disputed try which was awarded by the television match official after a lengthy study of the video, while there was the impression the ball had not been grounded correctly.
Evans converted the try and kicked a penalty while the Bulls replied with a try to prop Wikus van Heerden who drove through the middle of a ruck as the Auckland forwards moved to protect the flanks.
Keven Mealamu scored the Blues second try five minutes into the second half and the Bulls responded almost immediately driving van Heerden over from a lineout for his second touchdown.
After a second Evans penalty lifted the Blues to a 20-14 lead, the Bulls hit the lead for the first and only time.
Outstanding Bulls wing Bryan Habana took the ball on the halfway, stepped around an attempted tackle by Kurtis Haiau and outsprinted Evans in a race to the line before unloading to unmarked hooker Derick Kuun who scored.
But with eight minutes remaining Evans landed the drop goal that sealed the match for the Blues.
Drop Goal : Nick Evans
Venue : Eden Park, Auckland
Referee: James Leckie (Australia)
Assistant Referees : Brett Bowden (Australia), Josh Noonan (New Zealand)
TV Match Official : Ben Skeen (New Zealand)
Reviewer/Perf. Auditor : Stuart Beissel (New Zealand)†
1 Tony Woodcock, 2 Keven Mealamu , 3† John Afoa ,4 Kurtis Haiu ,5 Troy Flavell © ,6 Justin Collins ,7 Daniel Braid ,8 Jerome Kaino ,9 Danny Lee ,10 Nick Evans , 11 Rudi Wulf , 12 Benson Stanley , 13 Isaia Toeava , 14 Joe Rokocoko
15 George Pisi
Replacements: ,16 Nick White(FR) ,17 Bronson Murray (FR) , 18 Anthony Boric , 19 Nick Williams , 20 Taniela Moa , 21 Ben Atiga , 22 David Smith.
Substitutes: Bandise Maku, Werner Kruger, Wilhelm Steenkamp, Deon Stegmann, Heini Adams, Mornť Steyn, Hilton Lobberts.