The 33-year-old left fielder had started 46 consecutive games, although three of his last seven starts had been as the designated hitter.
"It's just spillover from playing a lot and sometimes you just need to take a half-step back and catch your breath a little bit," Scioscia said.
Scioscia said Hamilton wanted to play Saturday but the Angels chose to give him the day off.
"He was laboring to move [Friday], so it was obvious that it had gotten to a level where we want to err on the side of caution," Scioscia said.
Efren Navarro, who replaced Hamilton on Friday, started in left field on Saturday.
Matthew DeFranks is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.