His departure came with the Padres tied for last in the major leagues in runs and on-base percentage.
"It's a decision he came to on his own," said manager Bud Black, who had talked to his friend Joyner about his job in recent days. "Wally's a fine hitting coach. I thought he did a great job."
Joyner was preparing to go to Los Angeles on Tuesday when general manager Kevin Towers called to say the team preferred he not be there, said Joyner's agent, Barry Axelrod.
Axelrod said Joyner resigned due to "the frustration level with realizing that his philosophy, his approach, the way he wants to teach hitting just didn't coincide with what they like to see in the organization. He was hoping as time went by that they could somehow coincide or overcome that, but it became evident that was not going to happen."
Black said he would've supported Joyner returning for a second season. Instead, bench coach Craig Colbert will take over the role for the remaining games.
"We've all seen these guys for 156 games," Black said. "There will be a lot of dialogue will all our hitters."
Joyner was hired July 31, 2007, to replace the fired Merv Rettenmund. Joyner had previously served three seasons as a spring training instructor for the Padres.
The Padres will be looking for their fourth hitting coach in as many seasons.
Joyner was San Diego's first baseman when the Padres won the NL West in 1996 and 1998. San Diego reached the World Series in 1998, when they were swept by the New York Yankees.
He had a .289 batting average in his 16-season big league career, with 204 homers and 1,106 RBIs.