The D-backs five months ago declined to exercise options on the pair, but team president and chief executive Derrick Hall announced a reversal Monday, saying Towers and Gibson had been extended "beyond 2014."
The pair each had just one year left on their current contracts, which were signed after the D-backs won the National League West championship in 2011.
"We continue to be impressed by their loyalty, dedication, work ethic and track record of success during their big-league careers and are glad that their contract status will not be a distraction as we open up spring training this week," Hall said.
Gibson took over as manager during the 2010 season after the firing of A.J. Hinch and since then has guided the D-backs to a 290-279 mark. He was named NL Manager of the Year in 2011.
Towers took over for Josh Byrnes in September 2010.
The Diamondbacks completed their second straight 81-81 season in 2013.