By virtue of his victory, Brad Keselowski, who finished the race in 15th, also clinched his place in the Championship 4.
Hamlin led for 193 laps on Sunday and was in position to make a run for the win when he saw the 21-year-old Elliott come up on his bumper in the Final Stage.
During the ensuing pit stop, the jack on Hamlin's vehicle was dropped before all the lugnuts on the tire were secured.
Elliott confronted Hamlin on the cool-down lap at Martinsville and the two were heated after the race. Elliott's contact eventually led to Hamlin brushing the wall, and Hamlin's tire developed a rub.
Hamlin stays out, as does Kenseth (first), Elliott (fourth), Blaney (fifth) and Keselowski (seventh). He entered the race 19 points behind Brad Keselowski, who is fourth in the standings.More news: Morocco and Tunisia qualify for 2018 World Cup
But Kenseth's vehicle came to life within the final 15 laps.
Hamlin is one of five drivers trying to secure the last open spot in next week's championship race. Keselowski finished 16th, and while Chase Elliott finished second, Keselowski's points advantage proved enough.
Larson took the lead with a pass of playoff driver Denny Hamlin, who led 40 of the stage's 75 laps.
Championship contender Jimmie Johnson's chances of an eighth Cup Series title ended with a right-front tire problem that sent him into the wall with one lap remaining in the second stage.
Elliott finished second Sunday, failing to advance to the title race but was asked about nudging Hamlin out of the way.
Needing a win to advance to the Championship Four at Homestead-Miami Speedway on November 19, Hamlin took his vehicle to the garage. A win would lock him into the championship race automatically.