Luiten holed his second shot on the par-five 512-metre 10th at the Durban Country Club on his way to a five-under 67, and seven under overall, along with Tommy Fleetwood and defending champion Louis Oosthuzien.
The 227m iron shot was hit downwind, pitched on the front of the green and rolled dramatically into the hole.
"It was my first albatross. I hit a four iron and basically went straight at it and it just pitched exactly where I wanted, just in front of the green," Luiten told reporters.
"Then I hoped it would just release up the slope and that's what it did. It went straight at the pin and it went in. It was a good feeling to say the least."
Only one albatross was hit on the European Tour last season, by Chris Doak of Scotland at the Madeira Open.
Luiten's five-under-par total was matched by Englishman Fleetwood, who hit six birdies in his round on a second day of blustery conditions at the rolling, coastal course.
South African Oosthuizen three times saved par in the closing holes with delicate chips out of the bunkers but missed a short putt on the last for the outright lead.
A birdie at the last put Frenchman Victor Dubuisson one shot behind the leaders after a second 69, while Italian Matteo Manassero, with a second round 67, was fifth on five under-par.
Overnight leader Raphael Jacquelin was one over par for the second round with two bogeys and one double bogey after on Thursday being the only player to complete a bogey-free round.
He is three behind the leading trio, along with Darren Clarke of Northern Ireland.
The elite 36-man field is made up of winners on the Tour over the last 12 months plus one former tournament champion and five multiple tour event winners given special exemption.
(Reporting by Mark Gleeson,; Editing by Tony Goodson)
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