Santos, who was the European Tour rookie of the year in 2012 after winning his first title on home soil in the Madeira Islands Open, fired nine birdies and no bogeys to finish nine under par, two ahead of Garth Mulroy, Rhys Davies and Richard Bland.
Mulroy was leading the South African contingent out to maintain their remarkable dominance of events on home soil.
George Coetzee's victory in the Joburg Open on Sunday means nine of the last 12 European Tour events staged in South Africa have been won by home players, with all four previous Africa Opens won by South Africans.
And although Coetzee was not in East London after withdrawing in order to prepare for next week's WGC-Accenture Match Play Championship in Arizona, Mulroy took up the mantle with an opening 64.
Mulroy carded six birdies, an eagle and one bogey to finish seven under par, while Davies recovered from a bogey on the first to fire eight birdies in his last 16 holes.
Bland produced a flawless round containing an eagle on the third and five birdies in a back nine of 30 as the players took advantage of the calm conditions on a course measuring just 6,632 yards.
That is extremely short by modern standards and with no wind blowing in from the adjacent Indian Ocean, a repeat of the winning total of 27 under recorded by former Open champion Louis Oosthuizen in 2012 was on the cards.
"It's always nice to start the week this way," Mulroy told reporters after his round. "Usually we don't get weather like this here, but I'm not complaining. The scores are definitely out there, you've just got to make some putts.
"I am pleased to be up there. I played okay on my first nine, but only turned one under. On the second nine I made a few putts and got it going.
"I think that on the front side of the course there are a few short par fours and with good shots you can make some easy birdies."
Davies won the Hassan Trophy in 2010 but has struggled to reproduce that form recently and lost his card at the end of 2012.
The Welshman said: "I haven't had the greatest form over the last couple of years, so it's really nice to have a good round under my belt.
"It was a lovely start this morning, I enjoyed it, and I'll try to do the same again tomorrow."