McKenzie, who missed earning a PGA Tour card by a stroke Monday in California, had a 17-under 199 total on the Huntingdale course.
Two-time Masters champion Bradley Hughes of Australia was second after a 66, and defending champion Robert Allenby of Australia was 14 under after a 68.
Lonard, trying to become the first player sweep the Australian Open, PGA and Masters, had a 67 to join Australian countryman Brad Kennedy (66) at 13 under.
Lonard, a regular on the U.S. tour, has won three straight events. He began the streak in the New South Wales Open on the secondary Von Nida tour and added the Australian Open and Australian PGA the last two weeks.
Lonard overcame a five-stroke deficit in the final round of the Australian Open to successfully defend his title, and rallied from three strokes back Sunday in the PGA.
'I don't think it really matters up until the last couple of holes tomorrow,' Lonard said. 'In the last three weeks I've gotten the right bounces at the right time. Whether you can get that right bounce four weeks in a row, who knows?'
The 37-year-old McKenzie returned to Australia early Wednesday following the six-round PGA Tour qualifying tournament.
'I don't really know what I'm doing here,' McKenzie said. 'I'm tired, but for some reason I've been playing OK. I've been hitting the ball well and getting it to where I want it to go.'
Ricky Barnes, the 2002 U.S. Amateur champion, was five strokes back after a 68, and fellow American Hunter Mahan (68) was another shot behind. Corey Pavin, the 1995 U.S. Open champion, also shot a 68 to finish at 10 under.