It took him one year with the surprising Cleveland Indians to bag the prize.
Francona and Clint Hurdle of the Pittsburgh Pirates won the Manager of the Year awards Tuesday after guiding their small-budget teams to charming turnarounds.
In a close vote by the Baseball Writers' Association of America panel, Francona edged old friend John Farrell of the World Series champion Red Sox 112 points to 96 for the American League honour.
"I have a feeling he wouldn't trade what they did for this any day of the week," Francona said on a conference call from Tucson, Ariz.
Hurdle was a runaway winner in the NL, selected first on 25 of 30 ballots after taking the Pirates to the playoffs in their first winning season since 1992.
"It is so rewarding for me to see what's happened, the synergy in the city," Hurdle said in Pittsburgh. "To be a small part of a group that's able to bring joy at so many different levels — that's what's rewarding to me in life."
It was the first Manager of the Year award for Francona even though — in an interesting twist — he steered the Red Sox to World Series titles in 2004 and 2007. During his initial season with the Indians, he directed them to a 24-win improvement and a late surge that produced their first playoff berth in six years.
Cleveland lost the AL wild-card game to Tampa Bay, but voting is conducted before the post-season.
Francona said he called Farrell, a longtime colleague and his former pitching coach in Boston, on Tuesday morning because he thought it was funny they were up against each other as finalists.
If they heard such news years ago, Francona said, "both of us would have laughed each other out of the room."
Hurdle also was quick with a self-deprecating joke after he won.
"There's guys laughing all over the place," he said in an interview on MLB Network. "The players know so many times this season we'd have a big series, getting together just trying to break the ice I'd tell them, 'Hey, look guys, you've got to step it up, play big this week because I'm going to get outmanaged. I can tell you one thing that's going to happen: I'll get outmanaged. So really step it up.' And they did. They believed me every series."
Just like Francona, the 56-year-old Hurdle won Manager of the Year for the first time. His highest finish had been third in 2007, when he led Colorado to the World Series.
Don Mattingly of the NL West champion Los Angeles Dodgers came in second and Fredi Gonzalez of the NL East champion Atlanta Braves was third.
"I'm grateful," Hurdle said. "But it's kind of weird."
The only other Pittsburgh manager to win was Jim Leyland in 1990 and 1992, the bookends to three consecutive division titles for the Pirates.
After that, they endured a record 20 straight losing seasons — the longest drought in any of the four major professional sports — before going 94-68 this year to capture an NL wild card.
Riding a wave of excitement from a rejuvenated fan base in a city finally enthralled by baseball again, Pittsburgh beat Cincinnati in the wild-card game before losing to league champion St. Louis in a division series that went the full five games.
"I know we're scratching the surface of something that's dynamic," said Hurdle, who has managed the Pirates for three seasons.
Hurdle was chosen second on the other five ballots and was the only manager picked on every one. He had 140 points in the 5-3-1 scoring system to 68 for Mattingly, who received two first-place votes. Gonzalez got three firsts and 43 points.
Mike Matheny of the Cardinals was the only other skipper to appear on an NL ballot. He was tabbed second by four voters and third by seven.
The 54-year-old Francona garnered 16 first-place votes to 12 for Farrell, who lifted the Red Sox from last place to first in the AL East in his debut season as their manager. Boston won 97 games, tied for most in the majors, one year after going 69-93 under Bobby Valentine.
Bob Melvin, last year's winner, received the other two first-place votes and came in third after his low-payroll Oakland Athletics won their second consecutive AL West crown.
Francona never received a first-place vote during eight seasons as manager of the Red Sox. He had never finished higher than fourth for this award in 12 years as a big league skipper, including his stint with Philadelphia.
After a messy split from the Red Sox following their 2011 collapse, Francona spent a year in broadcasting that he said helped him become more patient and less stubborn.
This season with the Indians was among his most fun in baseball, he said, and he loves the people he works for because when challenges arise "we tackle them together."
"Boston is, you're not really supposed to ever lose a game, and that's difficult to do," Francona said, adding the job there is "to manage all the noise that's around the team so the guys can play."
"You can't have all that passion and not have some of the headaches that come with it," he explained. "It's a little different in Cleveland because it's more just baseball, which I enjoy."
Cy Young Award winners will be announced Wednesday evening, and MVPs on Thursday.
AP freelance writer Jim Lachimia in Pittsburgh contributed to this report.