Clarke carded a three-under-par 69 in testing conditions at Durban Country Club to lie two shots behind leader Raphael Jacquelin, the Frenchman managing the only bogey-free round of the day.
Jacquelin defied strong crosswinds blowing in from the Indian Ocean to post a flawless 67, one shot ahead of defending champion Louis Oosthuizen, with three of his five birdies coming in the last five holes.
Playing partner Colin Montgomerie, who usually plays on the Senior Tour since turning 50 last year, finished two under, while Clarke carded five birdies and two bogeys for his 69. The former Open champion has lost almost 3st since October as he looks to reproduce the golf which brought him a first major title at Royal St George's in 2011.
"My objectives are getting back to playing some of the golf I know I can play," the Northern Irishman said. "I have had a frustrating last couple of years where I have not played that badly but made stupid mistakes.
"I took a look at myself in October and thought I was getting too fat, too heavy, too lethargic and decided to do something about it. I spend a lot of time in the gym doing heavy weights, no cardio, and changed my diet and hopefully I will reap the benefits."
Montgomerie was also inches away from winning a Volvo Backhoe Loader - worth $75,000 - for a hole in one on the par-3 15th, although the Scot admitted he would have instead asked the tournament sponsors for the cash and split it with caddie Alistair McLean.
The former Ryder Cup captain added: "I was playing well at the end of last year and I started to play a lot more golf. I had not been having much fun on 7,500-yard courses on the main tour but I am a member of three tours now (the European Tour and two seniors tours) and it's given me more freedom to choose courses I can get round.
"It's very difficult and tricky out there. The wind was coming off the sea and made every hole a crosswind. You have to be very careful, you can make a mess out there in a hurry."