He ranks among active southpaw leaders in wins (13th), complete games (14; 13th), shutouts (eight; tied for ninth) and strikeouts (1,187; 12th).
Vice president/general manager Kevin Towers made the announcement, happily latching onto a pitcher who has driven the Padres batty over the years.
"We think he'll be a fine addition," Towers said. "I've always been a fan of his."
Estes is 13-5 with a 3.52 ERA in 23 career appearances against the Padres.
The 6-foot-2, 219-pound native of San Bernardino, Calif., split two decisions against the Padres in 2005 with a 2.57 ERA in two starts.
In four career starts at PETCO Park, he's 1-1 with a 2.67 ERA in 27 innings.
Estes' best season was 1997, when he was 19-5 with a 3.18 ERA in 32 starts for the Giants, putting him on the NL All-Star team. He has visited the disabled list seven times with shoulder problems but has been free of shoulder woes since 2001.
"He's a fly-ball pitcher who should be effective in our ballpark, especially with our improved outfield defense," Towers said. "He can handle the bat, too."
He didn't show it in '05, hitting .069 in Arizona, but he batted .236 in Colorado in '04 and is a .158 career hitter with four homers. The right-handed Estes batted .206 with a homer and 10 RBIs for the Giants in 2000.
Estes was 15-8 with the Rockies in 2004 before choosing the Diamondbacks in free agency, with the Padres also in pursuit.
He turned down a scholarship from Stanford to sign with the Mariners as their first-round choice (11th overall) in the draft out of Douglas High School in Minden, Nev.
Estes likely would join Jake Peavy, newcomer Chris Young, Woody Williams and Chan Ho Park or Clay Hensley in the rotation, with Tim Stauffer, Dewon Brazelton and Rule 5 acquisition Seth Etherton also expected to make bids during Spring Training.