Allen, an American football player for the University of Oregon, pipped world silver medallist Ryan Wilson by five thousandths of a second to win the wind-assisted race in 13.16 seconds on a hot afternoon in Sacramento.
"I am pretty excited about it," Allen, a wide receiver who also runs track, told reporters. "I did not know I finished first when I crossed the finish line, until they announced it.
"Things started clicking in practice, feeling better, and going through things and running faster."
Defending world champion David Oliver claimed third in 13.23 with 2011 world champion Jason Richardson placed fifth in 13.27.
Ash had become the first man in the world this year, and the 15th to run under 13 seconds, when he clocked 12.99 seconds in the semi-finals. But he did not finish the final, tumbling to the track midway through the race.
Disappointment also befell former world champion Bershawn Jackson in the men's 400 hurdles. Jackson went down with a reported groin injury and veteran Johnny Dutch won the race in 48.93 seconds.
World silver medallist Jenny Simpson and sprinter Jeneba Tarmoh both looked strong in victories on the concluding day of the championships.
Simpson easily won the women's 1,500 metres in four minutes, 4.96 seconds and Tarmoh edged Kimberlyn Duncan to take the women's 200 in a wind-assisted 22.06 seconds. World bronze medallist Curtis Mitchell won the men's 200 in 20.13.
Gusting winds pushed Jeff Henderson to a big leap of 8.52 metres on his final attempt in the long jump, but the mark was wind-assisted, costing him the 2014 world leading distance.
Two time U.S. collegiate pole vault champion Sam Kendricks added the national title, clearing 5.75 metres as U.S. record holder Brad Walker slipped to fifth.
Duane Solomon won the men's 800 in a dominant 1:44.30 with Ajee Wilson the women's champion in 1:58.70.
American record holder Evan Jager clocked 8:18.83 despite the searing heat to win the 3,000 metres steeplechase and Kori Carter paced the women's 400 hurdles in 53.84 seconds.
- Sports & Recreation
- Athletics, Track & Field
- Ryan Wilson
- University of Oregon