Playing just the third European Tour event of his career, Rai fired seven birdies in a flawless round on the East Course at Royal Johannesburg and Kensington, with Waring recording nine birdies and two bogeys.
That left the pair two shots behind clubhouse leader Paul Peterson, the left-handed American completing a brilliant 62 on the West Course before heavy rain, on an already-saturated course, forced play to be abandoned for the day.
Rai missed out on earning full playing privileges via the Challenge Tour in 2016 by less than €3,000, and was only two shots away from gaining his card at the qualifying school.
The 21-year-old from Wolverhampton finished 45th in the Australian PGA Championship before Christmas and missed the cut in the World Super 6 in Perth last week, only arriving in South Africa on Monday.
“It’s my first week in South Africa and my first time on the course, but I played it Tuesday and played it Wednesday,” Rai said. “It’s been a good start to the week so far.
“My game was pretty steady throughout, really. I drove it well, hit a few greens, made a few putts and also made a couple of up and downs when needed, so it was really solid throughout.”
Peterson, who won the Czech Masters last season, added: “It was fun out there today. Making birdie on half the holes is never bad and bogey free to match.
“I put a new putter in play this week and it proved to be a good first round with it.
“I’ve been putting a lot of really good work in with my coaches and the consistency is getting better.
“I’ve always been someone who putted pretty well and hit good drives, but my iron play is improving, my wedge game is improving and when I’m missing greens I feel really really confident with what I’m doing around the greens.”
South African players have won seven of the 10 editions of the Joburg Open, with Jbe Kruger the best-placed home player after a six-under 65 on the West Course.
Pre-tournament favourite and 2014 champion George Coetzee was five under par after 13 holes of his round.