The world number one shook off a nervy start with the putter to move clear with a string of birdies on the front nine.
Woodland rallied on the inward half, but missed a critical short putt to win the 13th and cut the gap to one hole.
The pressure on McIlroy was released and the Northern Irishman sealed the title.
There was an edginess to both men early on in the round, as McIlroy putted poorly, while Woodland's driving accuracy deserted him.
The third hole epitomised the scrappy early play. First, Woodland suffered a fate familiar to all amateur golfers when, having already hooked his drive, he then hit a tree with his approach and watched the ball trickle back to his feet.
Yet McIlroy then three-putted and the hole was halved in bogey fives.
McIlroy, who turns 26 on Monday, soon tidied up his play and pulled away with four holes in succession to go to the turn four up.
However, Woodland steadied at the start of the back nine and wins on 11 and 12 cut the deficit to two, but he passed up a glorious chance on the 13th to heap pressure on McIlroy, missing from five feet.
The Northern Irishman took immediate advantage, winning the 14th to return to three up, and closed out the match 4&2 on the 16th green.
Earlier in the day, McIlroy won the final two holes with stunning play to end Jim Furyk's dogged challenge in the semi-final.
McIlroy - who needed extra holes to beat both Billy Horschel and Paul Casey in earlier rounds - was one hole down to Furyk on the 17th tee, but struck a pinpoint iron to seven feet and holed for a two to go all-square.
He then ran in a huge putt across the 18th green for eagle to seal his final berth.
In the consolation match, England's Danny Willett beat Furyk 3&2 to secure third prize in the tournament.
Rory McIlroy won his first WGC Match Play title with a 4&2 victory over America's Gary Woodland.