Beckley also made the most of the sunny conditions to post a 66 in round two to join Ferguson, who took advantage of an early tee-time to fire a flawless eight-under-par 64.
The pair finished at 13 under, but they will have a long wait to see if their one stroke lead holds up.
Play was suspended for 70 minutes at 14h20 due to the threat of lightning and was called off at 18h25 due to failing light. The second will resume at 06h30 and, following the cut to 65 and ties, the third round is scheduled to start at approximately 08h30 (subject to change).
Marquette University graduate Brandon Cloete finished a stroke off the pace after successive rounds of 66 and shares third with Stuart Grehan from Ireland, who became the third player to better the course record at the Gary Player championship layout.
Tshwane golfer Jason Smith set the record with an opening eight under 64, but his effort was bettered by Sweden’s Tim Widing, who fired a 63 early on Wednesday to finish at 11 under.
Grehan birdied 10 and collected two more birdies at 15 and 18 to turn three under and dipped to seven under with birdies at one and two and an eagle at the par-five third. The Tullamore golfer added another gain at five and a brace of birdies took him to 12 under.
“I shot 63 in an Irish College event at home, but this is my lowest round yet,” the 23-year-old said.
“And I’ve never shot a 29 either. I didn’t really have any expectations coming here, but I’m in it now.”
Beckley and Ferguson were equally pleased to be in the mix with two rounds to play.
The Scotsman led the field in the first round of the 2014 SA Stroke Play at Benoni Country Club and was the 36-hole leader at Port Elizabeth Golf Club last year.
“I tied for 19th in Benoni and seventh last year, so at least I’m moving in the right direction,” joked the 19-year-old Bearsden golfer.
“I’ve got my brother Lewis out here with me and a good friend of ours, Cameron Kirkwood, on the bag. I struck the ball well in the first round, but I didn’t hole any putts and Cameron knows that when I get frustrated, I can try to get fancy.
“He told to keep doing what I’m doing, because the putts will start to drop. I only had two birdies on my front nine at the two par fives (13 and 18), but the putts started dropping after the turn.”
Ferguson boxed a 30-footer for birdie two and holed a 10-footer for eagle at the par five third before back-to-back birdies at four and five moved him to seven under.
“It was nice to finish with a birdie at the ninth to put myself in the mix with two rounds to go,” he said.
“The leaderboard is logjam and there are more low rounds to come from the afternoon field. It is all setting nice for a big battle over the last two days.”
A well-laid game plan helped Beckley to an eagle and six birdies for a share of the lead.
“I worked out a game plan for the course during the practice round, but I wasn’t 100 percent certain that I had it right,” the Potchefstroom golfer said.
“Course management and positioning is so crucial at this course, though, so I just committed to the plan and didn’t try to re-invent the wheel.
“I still left a few putts out there and I was disappointed with the soft bogeys at 15 and 17, but overall, I’m happy with my performance so far. It’s great to be in contention.”
Smith, who lifted the title in 2014, is 11 under with three holes to complete, while Rowan Lester from Italy and last year’s Sanlam SA Amateur Championship finalist Jovan Rebula tied at 10 under with respective rounds of 64 and 65.