Mallett, now coaching Italy, says the Spriongboks have ended the series in "a worrying state" with peter de Villiers' experiment of making 10 changes for the thrid Test having backfired badly.
"The Lions showed the Springboks that the world champions are not as good as they thought they were," Mallett told the Daily Telegraph.
"The lesson is quite simple for Peter de Villiers and his coaching team: you cannot make 10 changes from the previous match and expect success. Some of the players who were given a big opportunity were disappointing.
"It was a further reminder that South Africa can get ahead of themselves. Jake White, the World Cup-winning coach, almost made the same mistake at France 2007 when he fielded a mixed-up team for the pool game against Tonga and at half-time had to rescue the situation by bringing on his No 1 players.
"De Villiers did not rush to make wholesale changes until midway through the second half. He had also lost another of his main men, Fourie du Preez, to injury at half-time.
"The Springboks have finished the series in a worrying state. They played their best rugby in the first half of the opening Test in Durban and since then have been anything but consistent.
"They did play well to win the second Test, by putting together a great finish, yet have combined to give De Villiers and his team of coaches all kinds of headaches. They have regressed and it is worrying."
Mallett claims the lack of strength in depth in South Africa means that the Springboks' top team is miles ahead of their reserves.
"South Africa need to realise their 1st XV is appreciably better than the team which started this final Test. There is quite clearly not the strength in depth that they thought they had," added Mallett.
"The players they brought in were disappointing - some of them were innocuous and flaky. Full-back Zane Kirchner, wing Jongi Nokwe, lock Johann Muller and hooker Chiliboy Ralapelle all struggled - the team looked very disjointed and thoroughly disrupted.
"The truth about the Springboks is that if they are to function properly they need Bakkies Botha and Victor Matfield together at lock. The pair are the engine of the team and generate immense power."