A poll of all the team heads carried out by Britain's Autosport magazine, with each asked to list their top 10 and award points according to grand prix scoring, placed Alonso first with 269 and Vettel second on 198.
Alonso lost out to Vettel by three points on the track after the season's finale in Brazil last month.
The team principals' scores were kept secret but the magazine said eight of the 12 chose Alonso, who had the biggest winning margin in the five years since the top 10 was started, as the best driver.
The Spaniard, who won his two titles with Renault in 2005 and 2006, was also voted best driver in 2010 when Vettel took his first championship.
Lewis Hamilton, who is moving to Mercedes from McLaren, finished third in the poll (177 points) with Kimi Raikkonen fourth for Lotus (176) and McLaren's Jenson Button fifth (104).
"I was pleased to be chosen by the team principals as the best driver of 2012," Alonso told the Ferrari website (www.ferrari.com).
"I think it will be very difficult to repeat what was almost a perfect season this year, but we will try...Of course, next year I would prefer to win the title, happy to leave this prestigious yet idealistic award to one of my peers."