Coetzee opened with a 68 and threatened to establish a commanding lead with a second round 70, but Van Zyl cut his advantage to two strokes and took sole second on four-under-par 140.
He leads by two from Justin Harding and former Masters champion Charl Schwartzel, who returned respective rounds of 71 and 74 to tie for third.
Following a 10 month break after double knee surgery in April last year, Van Zyl eased his way back into competition with a tie for 55th at the South African Open Championship in early January.
A tie for third at the Dimension Data Pro-Am, followed by a joint runner-up finish in the Joburg Open in February signalled a speedy return to form for the 13-time Sunshine Tour champion and the Dainfern golfer sealed his spot in the field for the Investec Cup with a tie for sixth in the Africa Open and share of 15th in the Tshwane Open on Sunday.
Van Zyl won the Investec Cup on the back of podium finishes in the Dimension Data Pro-Am and Telkom PGA Championship in 2013, however, the former champion is not entertaining thoughts of another victory just yet.
“The body has a lot more wear on it than two years ago, so I am just happy to be in it,” he said.
“To be honest, I just wanted to hang around over the two days at Millvale, because it’s a very tough layout, but now I am in a good position to attack on the weekend.
“I was happy with the way I hit the golf ball and I started to get my head around those greens. I think you score better as you get to know the course and the guys who play here more regularly definitely had an advantage.
“Going to the Lost City Golf Course for the next two rounds levels the playing field, though.”
Van Zyl only had one black mark on an otherwise flawless card.
“I capitalised where I could, especially after a bad patch at six and seven,” he said. “I hit a great tee shot at the sixth, straight down the fairway and I thought I had the perfect yardage in, but I pitched my approach straight into the water.
“That was a little frustrating, made even more so when I missed a four-foot putt for birdie at the seventh. I just tried to limit my mistakes and did a pretty good job keeping the bogeys to just the one.
“The pins were more accessible and the greens were more receptive after the overnight rain. Overall, I was happy with the way I played the course.”
Asked what it would take to win at the Lost City, Van Zyl replied: “Patience, a hot putter and more patience.”
Fellow Lumenrock International Sport Management player Shaun Norris returned a 73 to slip to a tie for eighth on even-par 144, while Keith Horne also carded a 73 to finish a further stroke adrift.
Louis de Jager improved six stroke on his opening 78 and the even-par 72 lifted him to a tie for 20th on six over 150.