Embiid, who leads the Sixers with 23.9 points and 10.9 rebounds in 27 games, was hurt Saturday when he took a hard fall against the Suns.
Embiid used a soft touch to sink a couple of shots during pregame drills, and that was enough to convince the Sixers he could play through the injury.
The Sixers had already announced their starting lineup with veteran Amir Johnson at center before they made the late change.
Spurs coach Gregg Popovich decided to sit five players on Wednesday night with his team playing the second of back-to-back games: Manu Ginobili (rest), Danny Green (tightness, left groin), Kawhi Leonard (rest), Tony Parker (rest) and Rudy Gay (right heel).
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