He was two shots ahead of Simon Dyson and Marcus Fraser, who both shot 8-under 64s on a day of low scoring.
Dougherty had a string of seven straight birdies'the last three holes on the back nine and first four on the front'on the 6,972-yard Kota Permai course in the event sanctioned by the European and Asian tours.
Malaysias Danny Chia was among four players tied at 7-under 65, along with South Africas Keith Horne, Denmarks Soren Kjeldsen and Argentinas Daniel Vancsik.
New Zealands Mark Brown, coming off consecutive victories in India in the Asian Tours SAIL Open and the co-sanctioned Johnnie Walker Classic, matched Swedens Peter Hedblom, the winner last year at Saujana, with a 66.
Former U.S. Open champion Michael Campbell recorded three double-bogeys and one triple-bogey on his way to a humbling 12-over 84 that put the New Zealander 6 shots off the next worst player.
Northern Irelands Darren Clarke shot a 69 on Thursday.