Johnson had an advantage after winning the pole Friday and finished fifth. His boss, Rick Hendrick, the head of Hendrick Motorsports, missed the race due to an undisclosed family emergency.
Hamlin's victory was his fourth in 2009. Jeff Burton's second-place finish was his best this season.
"It takes awhile to sink in because I haven't let my mind think about it (but) to win four championships in eight seasons is amazing," Johnson said in a post-race interview. "I felt we had a shot late in the summer, but I was devastated after Texas (a 13th place finish at the Dickies 500)."
Kevin Harvick was third and Kurt Busch fourth in Sunday's race.
Mark Martin, 50, finished second in the points chase and Jeff Gordon was third.