A San Diego-area memorabilia store advertised three baseballs with Latos' signature and the words "I hate SF" below. The balls sold for $1,100, with half going to the Major League Baseball Players Alumni Association.
Latos and the Padres were eliminated from playoff contention by the Giants on the final day of the season last year. The Giants took the NL West title over San Diego and went on to win the World Series.
Latos said he only intended to raise money for charity and meant no harm with the autographs.
"I did it all in fun," he said Wednesday. "No disrespect to them. But it's not going to matter what I say because people are going to take it however they want."
Latos, who turned 23 in December, took the loss in the season finale at San Francisco but was a big reason the Padres were such a surprising success last year. The right-hander went 14-10 with a 2.92 ERA and 189 strikeouts in 31 starts. He also established a major league record by making 15 straight starts of five or more innings with two earned runs or less allowed from June 10 to Sept. 7.