The 33-year-old, who has two previous wins on tour back in 2018, shot up the leaderboard on Thursday with his birdie burst and overtook Dane Jacob Skov Olesen, who carded three birdies and an eagle in a bogey-free 67.
"After bogeying the second hole I was worried it was going to be one of those Thursdays again," Pepperell said.
"But I turned it around really nicely and played very well to be honest. So I'm very pleased."
There is a pack of six players a shot further back on four under-par, including a trio of South Africans in Jacques Blaauw, Wilco Nienaber and Jayden Schaper.
The two Australians in the field had a disappointing start, with Daniel Gale shooting a mixed-bag 76, which featured four double-bogeys and five birdies, and Danny List recording an eight-over 80.
Early starter Olesen had led for most of the day and with the wind causing problems in the afternoon, no-one looked likely to catch the Dane until Pepperell's late burst leapfrogged him into first place.
Pepperell, who suffered the disappointment of missing out on his card by one shot at the DP World Tour Qualifying School last month, had wife Jen as his caddie as his fortunes changed.
"It's been a while since I've been in a position where you're three, four, five under par at the top of the leaderboard - even on a Thursday," said Pepperell.
"So sometimes it can get in your head and it could have done but I just tried to keep my head down, focus and keep doing what I've been doing on the range yesterday and today, and it seemed to work."
