Derrick Hall, the club's CEO, confirmed that Gibson and Towers each received three-year contracts with club options for two more seasons. Those deals could keep both in place in Arizona through 2016.
The deals replace the existing deals that Gibson and Towers had.
Gibson, in his first full season as manager, led the D-backs to 94 victories this season, as they ran away with the division. That came on the heels of back-to-back last-place finishes by Arizona, which lost 97 games in 2010.
The D-backs pushed the Brewers to five games in the NL Division Series before falling in extra innings in the winner-takes-all finale.
"I have always been impressed with KT's relationship and experience and ability," Hall said on Thursday. "But this year, I was absolutely blown away with Kirk Gibson. ... He proved that he's going to be one of the elite managers in this game.
"The results on the field were nice and unexpected, but watching the dynamic between them [Gibson and Towers] was a sign for extreme optimism."
Gibson, praised by his players this season for his intensity and attention to fundamentals, took over as interim manager in 2010 after A.J. Hinch was dismissed.
"He's one of the most prepared managers I've ever been around," Hall said.
Gibson has already been named The Sporting News' National League Manager of the Year, and he figures to win the same award from the Baseball Writers' Association of America later this month.
"When an opportunity presented itself to me to be the manager of a ballclub, I had to put my stamp on it," Gibson said during the postseason. "And my stamp is what I learned through all my years in the game."
Gibson and Towers went about trying to change the culture of the clubhouse, and they succeeded beyond anyone's expectations.
Towers, hired in September 2010, revamped the bullpen, bringing in closer J.J. Putz on a two-year, $10 million deal, and he traded for setup man David Hernandez. He also helped to improve the team's depth with several key acquisitions.
Gibson brought discipline to the clubhouse and spent Spring Training preaching the value of mental toughness.
The result was a team that led the Majors Leagues in come-from-behind wins -- and one that surprised nearly everyone in winning the West.
"To me, I feel very fortunate to have Kevin Towers and Kirk Gibson as part of my team," Hall said.