Harrington, who won the British Open July 20, posted a 3-under 277 for a two-shot victory.
Sergio Garcia closed with a 68 and Ben Curtis with a 71 to share second place at 1-under 279.
Camilo Villegas (68) and Henrik Stenson (72) tied for fourth place at 1-over 281. Steve Flesch (69) was sixth at 282.
The Irish star is the first European to win consecutive majors.
"Obviously things like that will take time to sink in," Harrington said. "At the moment, I'm just enjoying the PGA win for the PGA win. I really did like the fact that no other European has won two majors consecutively. I hold a lot of European players who I grew up watching in high esteem. To believe that I achieved something they hadn't, is very special to me."
Harrington is the world's third-ranked player, behind Woods and Phil Mickelson.
Mickelson, who won the PGA title in 2005, shot a final-round 70 and finished in a seventh-place tie at 4-over 284.