McIlroy covered the three-hole aggregate play-off in one over par, but that was comfortably enough to beat Spaun in a somewhat anticlimactic finish at TPC Sawgrass.
A two-putt birdie on the par-five 16th gave McIlroy a one-shot advantage after Spaun could only make par after finding rough off the tee and a bunker with his approach.
McIlroy then safely found the green on the treacherous 17th before Spaun, who looked unsure of his club selection in the windy conditions, flew his tee shot over the green into the water.
The resulting triple-bogey effectively ended the American's chances of a second PGA Tour victory, even though McIlroy surprisingly three-putted from 30 feet.
McIlroy also bogeyed the 18th but Spaun still had 10 feet left for his own bogey and did not complete the hole after McIlroy tapped in.
Following his victory at Pebble Beach in February, it means McIlroy has won twice on the PGA Tour before the Masters for the first time in his career.
The world No.2 needs a victory in the year's first major championship at Augusta National to complete the career grand slam.
McIlroy had started Sunday's final round four shots behind overnight leader Spaun, but carded 68, briefly taking the lead before Spaun rallied. The American almost won the title in regulation as his birdie attempt from 30 feet on the 18th pulled up just three inches short.
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