England's hopes of making a winning start in the three-match series in Durban were scuppered as they went down to a battling 22-17 defeat at Kings Park.
Lancaster's men coped admirably with the Springboks' physical approach throughout a first half that ended 6-6 but the hosts edged away with tries from Morne Steyn and captain Jean de Villiers after the break.
The teams will now move on to the altitude of Johannesburg for the second Test next week.
Lancaster said: "Well done to the Springboks on the win. It was a tough test for both sides and I thought both sides competed really well, but the Springboks came out on top.
"From our point of view, I was really pleased with the first-half performance. There are a lot of positives to take.
"The critical area for us to work on is that third quarter where the Springboks controlled the game well and scored their two tries.
"I am delighted with the comeback at the end and the mindset we showed to keep playing.
"For a lot of young players out there, and the new caps, there were some fantastic performances all round.
"I am really pleased with a lot of aspects of the game. There are one or two areas to work on but lots of positives as well, so we will go in really good heart to Johannesburg."
England's points came from four Owen Farrell penalties and a superb - albeit by then in a lost cause - try from Ben Foden after the final hooter.
Lancaster was pleased with the performances of debutants Joe Marler and Tom Jackson and feels the team will be better for the run-out.
He said: "I thought in the first half we moved the ball well and challenged the Springboks defensively.
"We kept the ball alive and there were definitely periods of time when they were finding it hard to get reorganised defensively.
"Obviously the Springboks will learn a lot from the game, as we will.
"We have got a lot of young lads out there, the first time they have played at this intensity in this country, so we will learn a lot from it.
"We will keep positive in the way we approach it."
One downside for England was the loss of Durban-born centre Brad Barritt in the second half with a facial injury.
Lancaster was unable to update on his condition.
He said: "I have not had any word yet. He has gone for further investigation, so I don't know.
"His eye closed up pretty quickly but we will have to wait and see."
Full-back Mike Brown, who was making his first England start for four years, will also be assessed after a bang to the hand.
South Africa coach Heyneke Meyer admitted England had given his side a stern test in his first match in charge.
Meyer was pleased to come away with victory after coming under fire from some critics in the country over his squad selection.
The former Leicester coach said: "We know England are very well prepared and they are a very physical side.
"We knew they would go out firing on all cylinders.
"There were a few nerves at the beginning with the new captain and the new caps but I am very happy with the guys.
"I thought we played really great rugby in the second half and we could have finished with one or two more tries.
"England are a quality side and will probably improve, so we will have to improve.
"This is just the first step in the journey. The second and third Tests will be much tougher but luckily the nerves have gone now."
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