His solo-second finish earned him $680,400 and provided enough points to move him past Bubba Watson in the Official World Golf Ranking, making Stenson the new world No. 2.
Watson spent the week inactive, withdrawing from the Arnold Palmer Invitational after learning of the death of a friend.
This is the second time Stenson has reached No. 2 in the world, after spending seven weeks behind then-No. 1 Adam Scott in May, June and July last year.
Speaking of Scott, he dropped from No. 4 to No. 5 with a T-35 finish at the API, switching places with Jason Day (T-17). The rest of the top 10 remained unchanged.
Further down the list, Matt Every's win propelled him from 96th in the world to 40th and secured him a trip to his second Masters.
As for those trying to crack the top 50 to punch their own ticket to Augusta, Jason Dufner currently sits in the 50th and final spot, although he has nothing to worry about. His 2013 PGA Championship victory has him in the Masters field through 2018.
Here is your OWGR top 10 for the week of March 22: 1. Rory McIlroy, 2. Henrik Stenson, 3. Bubba Watson, 4. Jason Day, 5. Adam Scott, 6. Jordan Spieth, 7. Jim Furyk, 8. Sergio Garcia, 9. Dustin Johnson, 10. Justin Rose.