It capped an outstanding 2016 for the 40 year-old from Gothenburg, who became the first Swedish male golfer to win a major championship when he won the British Open in July. He also took silver at the Rio Olympics, finishing two strokes behind gold medallist Justin Rose.
The announcement marking his award praised his "barrier breaking feat" in winning the Open, which was achieved with calmness and "technical brilliance".
Stenson, who is currently ranked fourth in the World Golf Rankings, said he was "proud and happy" to receive the award.
"I thought I had a good chance, absolutely," he said. "But it is never easy when you are comparing different sports."
Sörenstam had been the only golfer to have won the award previously back in 1995.
Other winners since the prize was first awarded in 1925 include famous names such as Björn Borg, skiers Anja Pärson and Ingemar Stenmark and athlete Carolina Kluft.
Stenson follows last year's winner Sara Sjöström, who won three medals in swimming at this year's Olympics, including gold.