Kennedy, who won 21 games in 2011 but has struggled this season, went to Padres in return for left-handed reliever Joe Thatcher and minor-league pitcher Matt Stiles.
Arizona, second the in the American League West to the Los Angeles Dodgers, also received San Diego's competitive balance Round B selection in next year's draft.
Kennedy, a former first-round pick, has managed just a 3-8 record with a 5.23 ERA this season for the D-backs.
Thatcher, 31, has gone 3-1 with a 2.10 ERA in 50 games for the Padres in 2013.
Stiles is 2-2 with 14 saves and a 2.08 ERA over 46 appearances for Class AA San Antonio.