The home side beat the Springboks 37-21 in a damp London and made it 10 wins from 10 games for the coach who took over after England's dismal showing in the World Cup last year.
It was also the first time in a decade that England has managed to beat South Africa, with tries from Jonny May, Courtney Lawes, George Ford and Owen Farrell.
Jones had branded Saturday's opponents "bullies" in the run-up to the game and his team made a poor start, conceding three penalties in the opening five minutes.
But England gradually made pressure tell and scrum half Ben Youngs made the plays that set up both Ford and Farrell to profit with tries.
The result is another low point for the Springboks who have now lost five of their last six Test matches.
But Jones was hardly glowing in praise after the game, telling reporters: "All in all we get a pass mark."
"We gave away silly penalties early on -- that shouldn't happen.
"We are pleased with the result; not beating South Africa in 10 years we are satisfied with the result but not the performance.
"We would have liked a clean sheet so we have got work to do."
South Africa: 'It's hurting'
Opposing coach Allister Coetzee was also disappointed with his team's performance.
"As a collective we are not happy and have to keep working at that," he said.
"It's hurting, it's tough times. The team doesn't give up and keeps fighting, I take comfort from that."
Foley tortures Scotland again
It must have felt like history repeating for the Scots who once more suffered another late defeat at the hands of the Wallabies -- and again from the boot of Bernard Foley.
The team lost by a single point to Australia, the game finishing 23-22 at Murrayfield, and just when the players were seeking revenge for the controversial exit from the World Cup in 2015. The Wallabies were given a dubious penalty right at the end of that match which secured the quarter final win.
It was again Bernard Foley who delivered the agony, kicking a conversion with just four minutes left on the clock.
Ireland eases past Canada
Fresh from a stunning victory over the All Blacks last weekend, Ireland continued in great from, beating Canada 52-21 in a crowd-thrilling game in Dublin.
Canada couldn't match Ireland's scoring throughout the first half and struggled to get over the gain line as the team tired in the second.
Two tries in the final few minutes -- first from Tiernan O'Halloran and then from James Tracey -- extended the margin of victory.
Elsewhere in the international fixtures, New Zealand demolished Italy 68-10 in Rome, and France thrashed Samoa 52-8 in Toulouse.
And in Cardiff, Wales defeated Argentina in a much closer encounter with the home team emerging 24-20 victors.