Waldorf has yet to win on the Champions Tour since becoming eligible for the circuit last August, but he has finished sixth or better in three of his last four starts. He challenged for the title in the year's first major last month before finishing tied for sixth at the Senior PGA Championship.
Waldorf completed 36 holes at the Shoal Creek Country Club at 9-under 135 while first-round leader Jeff Sluman stood alone in second at 136. Sluman's 71 was highlighted by an eagle at the par-5 third.
Two-time defending champion Tom Lehman was in a tie for 19th at 140 after shooting a 71. Bernhard Langer, leader of the yearlong points race on the Champions Tour, struggled to a 73 and was nine shots off the pace being set by Waldorf.