Sharapova had initially played down concerns over her availability in Brisbane after pulling out of a recent exhibition tournament in South Korea due to a neck concern.
But the reigning French Open champion pulled the pin on the Brisbane International for the third time after the right collarbone problem restricted her on the practice court.
Sharapova pulled out last year, only to storm into the Australian Open final.
Meanwhile, former French Open finalist Sara Errani suffered an upset 6-4 1-6 7-5 second-round loss to Slovakia's Daniela Hantuchova on Tuesday.
Fifth-seeded Italian Errani, 25, bowed out in a two-and-a-half-hour showdown with the former world No.5.