Dave Grohl interrupted his performance of the band's "Run" to recall watching Flint on the festival's main stage in 2009.
"That was the craziest s**t I've ever seen," he told the crowd.
Closing the track, he said, "That's for you Keith."
Flint was found dead at his Essex home in March. He was 49.
The Foo Fighters also headlined Reading's sister festival Leeds on Friday night, when the band was joined onstage by Grohl's daughter, Violet, and a Freddie Mercury lookalike, who they pulled from the crowd to help them with a cover of Queen's "Under Pressure".