Cabrera appeared in 90 games last season, hitting .232/.272/.300 while serving two stints on the disabled list with injuries to his left hamstring.
The move opens the door for Alexi Amarista, who filled in for Cabrera, to compete for the starting job during Spring Training, said general manager A.J. Preller.
"It was a decision we looked at from a bunch of different angles the last few weeks," Preller said of the decision to non-tender Cabrera.
"But the way Alexi played the last six weeks, and played well, gave us some comfort in knowing that we had some coverage there."
Cabrera was arrested in September on suspicion of driving under the influence of marijuana and was later charged with resisting arrest. He faces a maximum penalty of one year in jail if convicted of the misdemeanor. He is scheduled to be arraigned in San Diego on Monday.
Cabrera was on the DL at the time of the incident.
Cabrera was suspended by Major League Baseball for the final 50 games of the 2013 season for his role in the Biogenesis drug scandal. He made the NL All-Star team with a strong first half of the 2013 season, hitting .291/.373/.396.
He led the NL in stolen bases in 2012, with 44.
In parts of six seasons with the Padres, Cabrera hit .248/.319/.333 with 136 steals. He was selected from the Rockies in the 2008 Rule 5 Draft by former GM Kevin Towers, who was able to keep Cabrera on the big league roster the entire 2009 season.
Amarista filled in more than just admirably in 2014, finishing with seven DRS (defensive runs saved) in 73 games and 626 innings. Some questioned if he's ready for a full season at a premium spot, but he showed he can handle shortstop beyond a fill-in role.
"From the way Alexi ended the year, you give him a chance to come in and compete for the spot. We'll look at the market and look to give [manager Bud Black] some options," Preller said.
Amarista made a believer out of more than a few advance scouts who followed the Padres during the season.
"It's certainly the best I've ever seen him play shortstop," said one. "His arm looked stronger than I've ever seen it and he's much more under control than I've seen from in the past."
Jace Peterson, 24, could get a look as well. Peterson is a career .287 hitter in the Minor Leagues who hit .113 in 53 at-bats with the Padres last season. The team was encouraged by his play in the Arizona Fall League, and Preller mentioned his ability to play a number of infield positions.
Also on Tuesday, the Padres announced that they have tendered contracts to 32 players for the upcoming season. Seven players are already under contract -- right-hander Joaquin Benoit, left-hander Cory Luebke, infielder Jedd Gyorko, and outfielders Cameron Maybin, Carlos Quentin, Seth Smith and Will Venable.