Immelman's victory comes four months after he had a tumor removed from his back, and a year after he was stricken with a stomach parasite at the previous Masters. He entered the final round with a two-shot lead before expanding his cushion while he and the rest of the field battled 30-mile-an-hour winds.
Immelman was as many as six shots ahead in the final round before a double-bogey on the par-3 16 made things interesting. He closed with back-to-back pars to finish 8-under for the tournament.
Woods never made a serious charge, carding three birdies and three bogeys for a 72 that left him at minus-5.
Brandt Snedeker finished in a tie for third with Stewart Cink after entering the fourth round alone in second. Snedeker took himself out of contention with five bogeys on the front nine before completing a 77 for a 4-under total.