Carolina trailed 1-0 but scored four goals in the final 4:24 of the second period. Whitney needed only 1:40 to notch his second NHL hat trick and then helped set up Justin Williams' team-leading 28th goal with 2.6 seconds remaining in the period, sending the Bruins off the ice to a chorus of boos.
Carolina won for the third time in nine games and took three of four in the season series against the Bruins.
Hurricanes left wing Erik Cole had to be helped off the ice with an apparent lower body injury at 8:46 of the second period and didn't return. Last year, Cole missed the final 22 regular-season games and the first 23 playoff contests. He returned for the last two games of the Stanley Cup finals for the champion Hurricanes.
Rod Brind'Amour added an empty-net goal and had three assists. Cam Ward made 34 saves for Carolina.
Brandon Bochenski scored twice and Paul Mara had his second point in 12 games for Boston, which dropped its fourth straight at home and six of eight overall.
Bochenski gave the Bruins a 1-0 lead when he jammed the puck past Ward with 4:28 remaining in the first period. Bochenski was acquired in a swap of minor leaguers from Chicago on Feb. 3 and has scored three goals in two games since joining Boston.
Whitney has 23 points in 26 career games against Boston and leads Carolina with 64 points.
The Bruins have one regulation victory since Dec. 29.
Notes: Glen Murray and Marco Sturm returned to the Bruins lineup after missing one game. ... Bill Mosienko has the record for fastest three goals in a game when in 1952 he accomplished the feat in 21 seconds. ... Bruins D Brad Stuart has one goal in the last 23 games. He entered the game a team-worst minus 22. ... Peter Laviolette earned his 100th coaching victory.