Zirbel, from Boulder, Colo., covered the 19-mile course in Chattanooga in 38 minutes, 16 seconds. Bookwalter, from Asheville, N.C., followed in 38:33.
Nathan Brown of Covington, Tenn., was third in 38:57.15, just ahead of Lawson Craddock of Austin, Texas, in 38:57.92.
This is the first time men and women have competed at the championships in the same weekend. Carmen Small of Durango, Colo., won the women's time trial in 42:37, beating Kristin McGrath of Boise, Idaho, and Alison Powers of Pinecliffe, Colo.
The road race is Monday.