The crowd was waiting for the British singer to take to the main stage in Chicago, Illinois at round 2.30pm local time when festival organisers announced the evacuation in anticipation of a severe storm.
Festivalgoers were ordered to exit the Grant Park grounds and head to designated underground shelters, but they were allowed to return an hour later.
The organisers altered the schedule so no sets were cancelled due to the evacuation, but Ezra's show was cut down to thirty minutes after the music resumed.
He wrote on Twitter.com, "I'm sorry it wasn't as planned guys, but thank you so much for coming back and making me smile."
Another storm threatened to hit in the evening, so the running times of the later acts, including Florence + The MAChine and FKA Twigs, were also rejigged so the festival could close early.
Frontwoman Florence Welch writes, "Sorry we had to go... Thank you to Chicago and Mother Nature for an incredible show... One of the most beautiful sights I've ever seen from stage... love you Lolla."