Wiggins was handed the trophy after a year which saw him become the first Briton to triumph in the Tour de France, before going on to seal Olympic gold at the Games in London.
The 32-year-old received 492,064 public phone votes on Sunday night to claim the top SPOTY prize.
McIlroy came 10th out of the 12 finalists with 29,729 votes.
It followed a year which saw him established himself as the best golfer in the world, claim his second major title by a record eight strokes, top the European money list and become the first European to win four PGA Tour titles in the same season.
But it fell to Wiggins, cccepting his award from the Duchess of Cambridge - making her first public appearance since being treated in hospital for acute morning sickness - to thank the voters who backed him for the SPOTY title.
Accepting his award from the Duchess of Cambridge - making her first public appearance since being treated in hospital for acute morning sickness - Wiggins thanked the voters for backing him.
He was especially grateful to his grandmother for pressing redial "God knows how many times".
"It has been incredible. To do this and be part of this after what everyone achieved tonight makes it more special," Wiggins said, thanking his support network at British Cycling and Team Sky.
Heptathlon gold medal winner Jessica Ennis came second with 372,765 votes, with US Open winner and Olympic gold medallist Andy Murray third with 230,444.
Runner and double Olympic gold medallist Mo Farah came fourth with 131,327 votes, just missing out on an award.
"To sit in the crowd and listen to Andy, then Jess be announced ... Well, my thoughts were Mo Farah had won it. For him to not get a look-in is incredible," Wiggins added.
"It is something to tell my kids because I think Mo will go down in history like Lord Coe."
What a year. To be standing on this stage with the likes of these people next to me is incredible.
Lord Seb Coe later fought back tears as he was given the lifetime achievement award for his athletics career and in recognition of his role in bringing the Olympics and Paralympics to London.
"Nobody could have done this alone," he said.
"To the millions of people that joined our Games either at home or in the venues, as officials or spectators or volunteers right the way through to those athletes that performed at the very highest levels, it is really with all of you this evening that I share this trophy."
The Team of the Year award went to Team GB and Paralympics GB for their successes in the Games during the summer.
It was presented by Sir Roger Bannister to cyclist Victoria Pendleton, who said: "It is a once in a lifetime experience, it was an incredible atmosphere."
Coach of the Year went to Dave Brailsford, performance director of British Cycling and team principal of Team Sky, who trained Wiggins.
The Hellen Rollason Award for outstanding achievement in the face of adversity went to Martine Wright, who lost her legs in the 2005 London bombings and went on to compete in the sitting volleyball at this year's Paralympics.
She received her award from former Olympic heptathlete Denise Lewis and the police constable who saved her life, Elizabeth Kenworthy.
"I am absolutely honoured to be here. I count myself lucky to have survived that awful day, and that I've made an incredible journey, the last seven years," Wright said.