In a battle between the two top-ranked teams in world rugby, Ireland won the second Test 25-24 when replacement flyhalf Ciaran Frawley kicked a last-minute drop goal.
Speaking on SuperSport television, Mallett gave credit to Ireland and their coach Andy Farrell for the way they came back after being beaten 27-20 in the first Test in Pretoria.
"It was a brilliant Test match. It was very, very astute coaching," he said of the way Farrell prepared the visiting team at the end of a campaign that effectively stretched for a full year.
"They didn’t need to do any fitness training, they needed to relax. It was a lot of mental preparation."
Mallett said the match was a reversal of the first Test.
"We (South Africa) came out and shot the lights out in that first 40 minutes and put them under pressure (in Pretoria) and they did exactly the same to us this time."
But he was impressed by the way the Springboks came back after trailing 16-6 at half-time.
"It wasn’t by kicking the ball back, it was by running the ball back,” he said, with replacement fullback Sacha Feinberg-Mngomezulu beating defenders and getting the Springboks on the front foot, forcing Ireland into errors and conceding penalties.
Springbok flyhalf Handre Pollard scored all South Africa’s points by kicking eight penalty goals, six of them in the second half.
But having turned a 10-point deficit into a five-point lead with 15 minutes to go, the Springboks went on the defensive, according to Mallett.
“We tried to protect the lead," he said.
"Everything we did to get ahead we stopped doing. We started kicking downfield hoping to get territory but they decided to hold onto the ball.
"It’s just such a pity we didn’t carry on playing the way we had before that."
Mallett also pointed out that the Springboks had won three successive knockout matches by one point on their way to winning the World Cup last year.
"Just as those teams went away thinking of all the 'what-ifs', so the Springboks can think of those small margins," said Mallett.
'Why no third Test?'
Former Ireland flank, South African-born CJ Stander, said Ireland had controlled the narrative in "a great Test match".
Stander said it was unfortunate that the two sides will not meet again in the immediate future, with the Springboks not playing against Ireland on their end-of-year tour to the northern hemisphere.
With the series between the two top teams in the world tied up at 1-1, many were asking why there was no decider.
“We always knew this series would come down to special moments," said former Springbok captain Jean de Villiers.
"Two dropped goals right at the end to clinch it for Ireland... why do we not have a third Test match?"
Instead of preparing for a decider, the Springboks will field a much-changed team against low-ranked Portugal in their next fixture in Bloemfontein on Saturday.
