Busch, who won for the first time in 31 starts at Martinsville in a truck race on the 0.526-mile oval on Saturday, dominated in the premier division in bright sunshine but cool temperatures that never let the track get quite as sticky as it normally does.
He led 352 laps, the most since Bobby Hamilton led 378 on April 20, 1998.
Allmendinger was second, followed by Kyle Larson, Austin Dillon and Brad Keselowski.
The finish looked nothing like the leaderboard for most of the race, but Busch and teammate Matt Kenseth stayed out when a caution flew with 15 laps to go while the rest of the contenders pitted for fresher tires.
When the green flag flew, Busch sailed off, Allmendinger beat Kenseth to the inside position and Busch's Joe Gibbs Racing teammate got hung up on the outside and faded to a 15th-place finish.
It was a reversal of the events of the previous restart, with 34 laps to go, when Busch and Kenseth worked together.
That time, Busch restarted on the inferior outside, likely with an agreement that Kenseth would let him grab the top spot, and the two once again seemed to be the best cars.
But with 11 laps left, teammate deals were off, and Busch opted for the superior inside line.
Several other drivers who pitted started in the sixth row, or worse, of side-by-side racing, and while Larson and Keselowski recovered for top-five finishes, others got caught up in traffic and that allowed Dillon to hang on out of nowhere.
It was the second straight race on the oldest, shortest race in the premier series that was a huge disappointment for Kenseth.
Last spring, he crashed race leader Joey Logano with 46 laps to go, earning himself a two-race suspension. This time, he seemed poised to challenge Busch for the lead with 35 laps to go until a blown tire by Jamie McMurray caused a caution, bunching up the field.
The race also was a lost day for Denny Hamlin, one of the favorites going in and the defending champion.
Hamlin was running fifth after 221 laps after overcoming a pit road penalty until his car lost control heading into Turn 1 and slammed into the wall, sending him to the garage. He never returned, and finished 42nd.
Kyle Busch grabs first Cup win at Martinsville
Kyle Busch sweeps the weekend at Martinsville, culminating with his first victory in the Cup series at the track.