The South Africans led 19-0 at half time, but the New Zealanders closed with two tries to Andrew Newstubb and Scott Curry, before the Boks sealed the game with a late try.
The All Blacks Sevens, who were rattled in the first half by South Africa's showing, clawed back into the game in the second period.
After winning five tournaments last season en route to the World Rugby Sevens Series title, it was more of the same from the BlitzBoks in Dubai this weekend as they bagged the title - for the second year running - after downing New Zealand in the final on Saturday.
England had opened the day with victory over Australia through Glover's try with the final play of the game, though the rub of the green eluded them in the 14-5 defeat to New Zealand.
The series next heads to Cape Town on 9 December.
Kenya collects 10 points at opening Dubai 7s
"We deliberately didn't put the guys into anything like this in pre-season as it's such a long season for us so it was always going to be a little bit of a risk".
Jeffery Oluoch powered over from a turn over ball to put Kenya ahead, but his celebration was cut short by Seabelo Senatla, who latched onto a loose ball in the middle to draw level before he grabbed the brace for the tournament's champions. "We want to focus on our processes and if we leave the result and the result doesn't go our way then we're still happy", he added.
"It's easy to play well in a team as good as this‚" Smith said.
The Blitzboks breezed through the group stages, beating Uganda, Kenya and Canada.
After losing to New Zealand in the semifinal, England captain Tom Mitchell, said: "It's tough to take and terrible to lose but they seized their chances better than we did".