Nitties went into the third round with the lead by himself and stayed atop the standings by firing a 3-under 69. Day, who won a PGA Tour event in 1999 and finished 15th on the money list in 1999, stormed through the field with a 64.
That left the co-leaders at 15-under 201. Geoffrey Sisk was alone in third at 203.
The low 25 finishers and ties will earn their way onto the PGA Tour next year. The Jack Nicklaus Tournament Course and Stadium Course at PGA West are home to the event. Every competitor will play each course three times.
Tyler Aldridge (70), Bryce Molder (69), Jay Williamson (69), Troy Kelly (70), James Oh (70), Robert Garrigus (71) and Derek Fathauer (65) were tied for fourth at 204.
Mark Brooks, 47, winner of the 1996 PGA Championship, was tied for 11th.