The Padres also opted to non-tender two Minor League players on Thursday, second baseman Matt Antonelli and relief pitcher Luis Perdomo.
The Padres reached a pre-tender agreement with outfielder Chris Denorfia for $800,000 on Wednesday. Denorfia, 30, will essentially serve as the Padres' fourth outfielder and a bench player in 2011.
Gwynn, the son of the Hall of Fame outfielder by the same name, hit .204 and had an on-base percentage of .304 in 289 at-bats for the Padres last season. Gwynn missed nearly a month with a broken hamate bone in his right hand, an injury he suffered Aug. 18.
Gwynn had 11 hitless at-bats after returning from the injury, which required surgery, in September.
There's a chance the Padres could still re-sign Gwynn, possibly to a Minor League deal.
Hairston hit .210 with 10 home runs and 36 RBIs last season, hitting .133 after the All-Star break.
Hairston, who played for the Padres from 2007 until 2009, was reacquired in January from the A's with outfielder Aaron Cunningham in exchange for third baseman Kevin Kouzmanoff and Minor League second baseman Eric Sogard.
The Padres still have four arbitration-eligible players: Ryan Ludwick and pitchers Tim Stauffer, Mike Adams and Heath Bell.
The Padres tendered contracts to 33 players on Thursday. First baseman Adrian Gonzalez and Denorfia were already under contract. The team now has 35 players on its 40-man roster.
Antonelli, the Padres first-round Draft pick (17th overall) in 2006, missed all of the 2010 season while recovering from hamate bone surgery in his left hand. Antonelli hit .193 in 57 at-bats in September of 2008.
Perdomo was 1-0 with a 4.87 ERA in 36 games over two seasons with the Padres. He spent most of the 2010 season with Triple-A Portland, going 4-6 with a 3.40 ERA.