Suppan was 2-3 with a 5.28 ERA in six starts for the Padres. He allowed 15 earned runs in his past three starts after allowing three in his first three starts with the team.
"Moving forward on the starting pitching side, we've decided to go in another direction in that spot," Padres manager Bud Black said.
Suppan, who signed a Minor League contract the week before Spring Training, joined the team May 2 when his contract was purchased from Triple-A Tucson.
He won his first two starts, defeating the Brewers on May 2 and then the Rockies six days later. In his last start with the team, he allowed six earned runs in five innings -- including two home runs -- during Monday's loss to the Cubs at Wrigley Field.
Suppan wasn't available for comment Friday.
"He handled it fine," Black said of his conversation with Suppan on Friday afternoon. "He's been around long enough to know this is a business and there are hard decisions along the way.
"He thanked us for the opportunity. He did everything that we asked."
Eric Stults will pitch on Sunday, the day Suppan would have thrown. Stults will pitch on regular rest since Thursday was an off-day for the team.