Central Florida shot 16-under 268 and leads second-place Arizona by two strokes. South Carolina is tied for third at 273 with Charlotte.
The top five teams after 54 holes will advance to the NCAA Championships.
Arizona's Tarquin MacManus shot 8-under 63 to grab the individual lead by two strokes over Charlotte's Corey Nagy.
Henrik Norlander shot 69 to lead Augusta State and is tied for 14th. Teammates Taylor Floyd, Janne Kaske and Carter Newman shot 71 and are tied for 30th. Jake Amos shot 72 and is tied for 45th.