McIlroy succeeds Luke Donald as winner of the coveted award, having also replicated the Englishman's previously unprecedented achievement of winning both the Race to Dubai and US PGA Tour money list in the same season.
"Everyone who knows me knows how special the 2012 season was," McIlroy said. "A couple of wins, including a major, and consistent performances in big events all helped me win The Race to Dubai for the first time. To win that was a massive highlight of an amazing season and I hope it will be the first of many."
He added: "Now, to have been named as The European Tour Golfer of the Year puts the icing on the cake."
The 23-year-old from Northern Ireland captured his second major title in August, winning the US PGA Championship at Kiawah Island by a record eight shots, matching the winning margin of his maiden major triumph in the 2011 US Open.
McIlroy also won three times in America before playing a vital role in Europe's stunning Ryder Cup victory at Medinah, while he ended the year in style with five closing birdies to win the DP World Tour Championship in Dubai.
He added: "It is a very special honour indeed and you only need to look down the list of players who have preceded me as the winner of this award to see precisely why; quite simply, it is a Who's Who of golf and I'm delighted to now be a part of that in the history books.
"We play golf because we relish the opportunity to win major championships and world-class tournaments around the globe. But when we do that, to be recognised for these achievements is a great thrill and I thank all the members of the panel who voted for me."