The day off is just the second of the season for Beltran, who last sat on April 11.
"I was thinking about that ahead of time," Matheny said. "It works out well."
Beltran, who talked his way into the lineup on a scheduled day off during the team's recent trip to Chicago, knew midway through Wednesday's game that he would not be starting against Pittsburgh's Erik Bedard on Thursday. That was one of the reasons why Matheny didn't sub in for Beltran, as he did for several other starters.
Beltran, 0-for-5 against Bedard in his career, came in to pinch-hit with a runner on first and two outs in the eighth inning, but struck out to end the threat.