Eaks has a 128 through two rounds, the best two-round score on tour this year.
First-round leader Dana Quiqley is four shots back at 12 under. Bernhard Langer is at 11 under.
Severe weather halted play for nearly three hours, and tournament officials sent all spectators away, although a few came back.
The TPC Twin Cities received 1.25 inches of rain from the thunderstorms, softening greens for those who waited out the delay.
Eaks, who has one top-10 finish in 14 starts this year, went 6-under on his first 10 holes once play resumed to pull ahead. He also birdied No. 18 as darkness was quickly closing in.
Jones eagled the final hole.
Gary Hallberg (68), Hale Irwin (66), Lonnie Nielsen (66) and Ron Streck (64) are at 10 under, six shots behind Eaks.