Kite completed 54 holes at 10-under 203. Defending champion Adam Scott, Lee Westwood and Steve Elkington all had 69s to move into a tie for second place at 204. Also at 204 were Stuart Appleby (65), Luke Donald (67) and Ernie Els.
Kite is a 19-time winner on the PGA Tour and has seven victories on the senior Champions Tour.
"This is the only reason that I took this little challenge to come back and play the tour was to challenge myself and put myself in a position to see what I could do," said Kite"
Kite's last win on the PGA Tour was at the 1993 Los Angeles Open. The last time he held the 54-hole lead was in 1997.