Head coach Andy Robinson thought Scotland were "bullied" by South Africa during their 21-10 defeat.
"We've got a lot to learn in improving defence and in attack, particularly physically," he told BBC Sport.
"I felt they bullied us a little in the first half. They didn't have to do a lot to win the game because we gave them field position from penalties.
"They scored from a maul which makes me very, very angry and then from an interception."
The defeat means Scotland have no chance of being in the top eight of the world rankings before the draw for the 2015 World Cup and will therefore be included among the third-seeded sides.
Robinson now wants to see a reaction to what was a fourth consecutive home defeat, following last weekend's more punishing loss to New Zealand.
"Next week against Tonga we need a performance to put together the lessons they've learned from the first two games," Robinson added.
"There's a lot for us to look at. The disappointing thing from our side is we allowed a side to get a lead again and that's something you can't afford to do."
Scotland improved after the interval and saw a lot of the ball as they chased the game but all the hosts could manage was a well-worked try from a line-out for Henry Pyrgos.
"I thought South Africa defended superbly well," explained Robinson. "If they hadn't defended as well as they had, it could have been a different story."
Replacement scrum-half Pygros plunged over to score after latching on to a tap-back from Kelly Brown in a rehearsed move from a line-out.
A period of Scottish pressure followed but the ball was given away too often to trouble the formidable Springboks.
"Henry Pyrgos brought some real energy to the field and he took his chance well," said Robinson.
The Glasgow number nine, making his second Scotland appearance, was thrilled to score but frustrated not to have made it a closer contest.
"The try came off beautifully but we are all massively disappointed with the result," he told BBC Scotland. "It's a game we should have got more out of.
"First half, we didn't come out like we wanted to and in the second half we had chances to get more points on the scoreboard and we didn't do it.
"There were times when we didn't hold on to the ball when we needed to and we weren't accurate enough at the breakdown.
"It was very quick and physical - a definite step up for me. But you just go back to what you know and try to concentrate on the things you can do well.
"The crowd has been amazing for both games at Murrayfield and we are disappointed for them. It's going to be a huge week of training for Tonga. We need to go and get the win."
South Africa head coach Heyneke Meyer was delighted to follow up last weekend's victory in Dublin with another success.
"All credit to Scotland, they played superbly and just great, great defence kept them out," he said.
"It was not a great game but I'll take an ugly win.
"We know we can play much better but we mustn't take anything away from Scotland.
"They came out and gave everything for their country. I think they can be proud of what they achieved today.
"We're in a learning curve and I thought the guys didn't panic. Our defence was awesome."