Johnson, the 2007 Masters champion who entered the week with only one top-10 finish this year, had a 19-under 261 total on the La Cantera Golf Clubs Resort Course.
This hasnt been the best year for me, said Johnson, who earned $810,000. Its been a long time coming.
Wi finished with a 61, Wilson had a 63, and Wilkinson shot a 64.
Wi parred the final two holes.
I didnt look at the scoreboard until I got to the 15th hole. I knew Zach was close, but I was playing very good, Wi said. I was very happy to make those birdies on 15 and 16. I wish I could have made one more.
Third-round leader Rory Sabbatini shot a 72 to finish seven strokes back at 12 under.
Ive been working on my putting over the last six weeks with my teachers and it really paid off this week, Johnson said. I had a tough year, but the putts started to fall into today and that why Im at the top of the leaderboard.
He never trailed on the back nine, but both Wi and Wilkinson keep the pressure on with birdies putts of their own. On the par-4 18th hole, Johnson hit his drive more than 300 yards and put his 9-iron approach to 5 feet.
The ensuing walk up the 18th fairway was a filled with smiles and waves for the crowd, while his wife and young son waited behind the green.
Hopefully this is the first of many to come, Johnson said.