After defeats in the first two Tests, England ended their tour on a positive note by claiming a 14-14 draw in Port Elizabeth to avoid a series whitewash.
Yet after matching the Springboks in the power stakes, claiming a well-worked Danny Care try and having a late drop-goal chance to win it through Owen Farrell, Lancaster felt it was a missed opportunity.
He said: "We have mixed feelings in terms of the result.
"We are desperately disappointed not to have got the win.
"I was really pleased we improved our defensive performance from last week and I thought our mentality and mindset going into the game was strong - but we are disappointed not to have won, particularly having got into a position where we could have sneaked it.
"But credit to South Africa, they are a tough side to play at home, as everyone knows.
"On reflection for us, from the tour as a whole, there are a lot of positives we can take from it."
One particular positive was the performance of scrum-half Care on his return to the side at the Nelson Mandela Bay Stadium.
The 25-year-old was dropped for the Six Nations earlier this year after a series of off-field incidents and has been made to wait for his recall.
Lancaster said: "We are in a fantastic position in this country in terms of the quality of nines we have got.
"We lose Ben Youngs, who had an outstanding second Test, then Danny Care starts the third Test and gets man of the match.
"That is not counting Lee Dickson who, throughout the Six Nations and this tour, has pushed both and could be considered unlucky not to start.
"I'm delighted with the strength in depth and really pleased for Danny.
"He has made his mark back on the international stage. It was his 33rd cap but it felt like his first again."
Farrell, who has been a substitute since a disappointing first Test performance, also impressed after coming on as an early replacement for injured fly-half Toby Flood.
The 20-year-old kicked two penalties, including one to tie the scores, after JP Pietersen looked to have given the Springboks a decisive lead with a try just after the hour.
Lancaster said: "Owen coming on off the bench did extremely well.
"He is disappointed he has not managed to win the game but that is the competitor he is.
"Overall I thought we withstood the attacking barrage that comes when they get possession and position.
"We were much better this time and that augurs well.
"In terms of experience we have gathered a lot but the boys in the changing room are ultimately disappointed they could not gather the win."
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