Englishman Willett, 29, nearly struck an eagle on the final hole for a better advantage but his six birdies give him an upper hand heading into the final round on Sunday.
The victor at Augusta past year, Willett was lurking at the start of play, having teed off with just a one-shot deficit to overnight leader Bernd Wiesberger.
Willett, who has struggled for consistent form since claiming his first major title at Augusta National past year, was part of a six-strong group three shots back on six under which included American Peter Uihlein and Hong Kong Open victor Sam Brazel.
Wiesberger ended the day one over the card, having lit up the Saujana Golf and Country Club on Friday.
"It was good, it s always nice to get out early when you re in Malaysia", said Willett, ranked number 15 in the world.
'I holed a couple of nice putts when I needed to. However, three dropped shots on the next four holes and a woeful triple-bogey at the ninth left him six shots off the pace.
"One or two under par is a good knock out there, and there's a few guys that can go low if it's windy".
"I'm not sure what will win it to be honest, it depends on if we pitch up and it's flat calm", he said.
"My last birdie before 18 was on 10 so I'm happy to have made that". I'm playing pretty well and giving myself opportunities.
"It's not been the start I would have wanted to the season with how things have been but we're still doing the same, still working hard, still training hard, not trying to do anything different. I just hit them pretty close and felt like I had a good idea of what the ball was going to do on the green today again, which was nice".
The nine consecutive birdies would have stood as a record on the European Tour but because lift clean and place was being used today it can not be classed as official.