The 86km second stage took riders from Wilderness to Mossel Bay and the ASG-Ellsworth outfit made a break up Outeniqua Pass to create a buffer of nearly nine minutes.
They crossed the line in 3:15:01, three minutes ahead of the French-German pairing of Antonin Marecaille and Julian Biefang (Chiru-Magura-Canyon).
Third on the day were Norwegian professionals Eirik Fiskvik and Thomas Engelsgjerd (Happysalmon), seven minutes behind the leaders.
With an overall time of 5:38:48, the Durban-based Marais said their objective was to try to ride within themselves and to take the opportunities when they arose.
“There was quite a big group for about 15km, but once we started the dirt road sections, we broke away with Marecaille and Biefang,” he said.
“We rode quite comfortably together and then up Outeniqua Pass we could see one of them was struggling a bit.
“We did not go too hard, but maintained a steady tempo and managed to break away.”
He said it would be more of the same tomorrow on the 102km third stage from Hartenbos to Riversdale.
“We have a really good cushion over the second team, so it is going to be a case of not blowing our position.”
Belgian Kristof de Neys and British partner Catherine Williamson (LawPack) stayed on top in the mixed category after winning the stage in 3:50:48.
Williamson, last year’s mixed champion, said they felt “nice and strong” at this stage of the race.
“The day went really well and there were no mishaps. We know each other quite well, so riding-wise it’s working out nicely.”
The 614km race, supported by STANLIB and Volvo Cars, takes riders through many of the Western Cape’s iconic trails before ending at La Couronne Wine Estate in Franschhoek on Saturday.