"It came down to a race off the last hurdle and I came out on top," Allen told reporters.
"I've been working on my speed so I knew if I was in the race the last hurdle I would have a chance and that's what it came down to."
World record holder Aries Merritt finished fourth in 13.52, just behind Jarret Eaton (13.51) in a race run into a head wind.
Morris had just missed her only attempt at a 2018-leading 4.94m when the competition was halted because of the impending storm and she decided to call it a day.
"All day we had a toss up with the weather," the world silver medallist told NBC Sports after winning the event at 4.80m.
An anticipated challenge by Jenn Suhr fizzled early as the 2012 Olympic champion went out at 4.60m to finish behind Katie Nageotte (4.70).
Wind played a big role in the performances, Morris said.
"We had swirling winds and head winds, which really affect you in the pole vault because your pole is pretty much like a sail," she said "You catch the wind and it messes up your un a little bit."
A large field did not help either.
"It took a hour and a half before I even took my first jump," Morris said.
"Then I got in a really good roll," she said of five consecutive first-attempt clearances. "Then at the end I had to be cut short."
Her only miss before the failure at 4.94m came on her first attempt at 4.55m.
Before the rains came, former world silver medallist Shamier Little posted the second best women's 400m hurdles time of the year (53.61 seconds).
Iowa native Shelby Houlihan, who won the 1,500m on Saturday, gave the small Des Moines crowd something else to cheer about by winning the 5,000m in 15:31.03.
The usually fast 200m finals were hampered by head winds with Olympian Jenna Prandini (22.62) finishing ahead of world 400m champion Phyllis Francis (22.83).
The men's race went to Ameer Webb in 20.47, with world indoor 400m record holder Michael Norman not running.
Olympic silver medallist Evan Jager earned his seventh consecutive U.S. 3,000m steeplechase title in 8:20.10.
The championships' winners in the field events and races through 1,500m are eligible for the July 14-15 Athletics World Cup in London. The U.S. team is expected to be named this week.
(Reporting by Gene Cherry in Raleigh, North Carolina; Editing by Peter Rutherford)
Share
