McGuiness looked shocked when co-hosts Tess Daly and Claudia Winkleman announced his name.
He was not the best on the night, but the public vote secured his win.
Aliona's the first pro to win the show twice
"I feel spaced-out, really weird. It's been one of the most special things I've ever done," he said.
EastEnders' Kellie Bright had to settle for joint runner-up alongside former Coronation Street actress Georgia May Foote.
The BBC soap star put up a good fight, with a maximum of 40 points for her first two dances and 39 points for her third.
"I'm glad I got to see it through to the end," she told the co-hosts.
Foote said: "I'm so happy. All I wanted to do was get to the final."
As expected, broadcaster Katie Derham and partner Anton Du Beke finished in fourth place.
Eliminated at the beginning of the results show, the 45-year-old was magnanimous in defeat.
"You've brought out the best in me and I really am forever grateful," she told her partner who was making his first ever appearance in a final after 12 years on the show.
Pop Star McGuiness had been the bookies' favourite to win for several weeks.
He opened the competition with a quickstep to My Generation, but made mistakes.
"It was quick, it was slick. Couple of incidents here and there," said head judge Len Goodman as he scored 36 points.
Partner Aliona Vilani offered to "take the blame" for the showdance which left the judges underwhelmed.
This segment contained the only dance in the series where there are no rules.
"I would have liked a bit more show in the showdance," said Goodman as the pop singer picked up 35 points.
Craig Revel Horwood agreed: "I was disappointed, I really was."
However, they made up for it with their paso doble to It's My Life, which scored 39 points.
"From week one, for me, you've been the most consistent," head judge Goodman told him.
"Goodness gracious, great balls of fire!" cried Bruno Tonioli.
"You're number one in my book," said Darcey Bussell.
Bright and partner Kevin Clifton topped the leaderboard after their three dances.
For the judges' pick, they performed a tango to You Really Got Me by The Kinks and scored the first 40 of the series.
"It was truly fab-u-lous, darling!" Revel Horwood exclaimed.
"Excuse the pun, but you've ironed out all the kinks," stated Goodman.
Bright and Clifton performed a show-stopping, Lindy hop routine which showcased a series of energetic moves and impressive lifts.
The couple chose their Star Wars-inspired Charleston as their favourite dance of the series and scored 39 points.
"You are one of the most exciting performers," said Revel Horwood.
Foote and Giovanni Pernice performed their rumba to Writing's On The Wall for the judges and scored 36 points.
"Totally smitten by the sex kitten. A little issue with balance," said Tonioli.
A passionate showdance combining elements of tango and Viennese waltz followed and earned 36 points.
"You're a lovely ballroom dancer," said Goodman.
Foote's final dance was her Charleston inspired by the musical Chicago.
Greeted with praise from the judges, she earned the maximum of 40 points.
"A sparkling cracker of a Charleston," Tonioli enthused.
Revel Horwood said he would have Foote in any of his West End shows, a compliment that reduced her to tears.
Derham and Du Beke earned 31 points for quickstep to 42nd Street. They picked up the same number of points for their showdance.
The star-studded final included appearances from this year's contestants, The Great British Bake Off's Mary Berry and chart-topper Ellie Goulding.