San Diego manager Bud Black said that Giles "tweaked his side" either last week diving back to first base on a pickoff attempt or on a check swing in the Padres' 7-5 victory on Friday over the Dodgers.
Paul McAnulty got the start in right field on Saturday with Scott Hairston hitting leadoff, the spot Giles normally occupies.
"Brian is going to get a couple days [off]," said Black, who said Giles would be available to pinch-hit or play in the field if need be.
Sitting Giles on Saturday and Sunday along with the off-day on Monday would give Giles three full days to recover from his side injury. Black said he was hopeful Giles would return Tuesday for the start of a three-game series against Colorado at PETCO Park.
Giles, who had microfracture surgery on his right knee in the offseason, is hitting .300 this season with one home run, six RBIs and a .375 on-base percentage.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.