The match was sweet revenge for Chiefs, who were beaten 2-1 by Amabhubesi on the opening day of the season in a shock result.
An early goal from Musa Nyatama had the hosts dreaming of a league 'double' over the Soweto giants, but it was not to be.
An equalising goal from Kaizer Motaung Jr, starting his first match of the season, and late winner from veteran winger Arthur Zwane secured a 2-1 win for Muhsin Ertugral's team that sees them move into the top four of the Absa Premiership table. Thanda got off to the perfect start when some poor defending from Chiefs' centrebacks, Mokete Tsotetsi and Thabang Rooi, allowed Nyatama easily to beat Itumeleng Khune from close range and put his side a goal up with just three minutes on the clock.
Zwane could have pulled his team level in the eighth minute, but he shot wide of goal from 10 metres out, much to the relief of former Amakhosi teammate Aubrey Mathibe in the Thanda goal. Two minutes later Abia Nale tried his luck from range, but the youngster's right-footed shot was well over the crossbar.
Thanda had a couple of chances to increase their lead, particularly Nyatama, who headed wide of goal from a Sibusiso Hadebe free-kick, but they were pegged back in the 28th minute when Zwane put Motaung Jr in, and the striker grabbed his first goal of the season to make it 1-1.
Chiefs' no.7 should have scored a second just before half-time, sending a left-footed effort from just six yards out wide of Mathibe's right-hand upright and leaving the teams level at the break.
Amabhubesi and Amakhosi exchanged chances early in the second half, with Reneilwe Letsholonyane and Nale both shooting off target for the visitors, while Thanda's Nyatama saw his effort parried away by Khune.
On the hour mark Mathibe did well to tip Zwane's drive over the crossbar, and Chiefs were then lucky to see substitute Nkosinathi Nhleko go just wide of goal with two separate efforts, one with his left foot and one with the head, as the end-to-end action began to stretch the respective defences.
The sides contrived to create more scoring chances as the final whistle approached, particularly with shots from long range, but all too often they either failed to hit the target or they were mere catching practice for 'keepers Mathibe and Khune.
However, Nale turned the game in Amakhosi's favour with some wonderful skill in the 85th minute, taking three defenders out of the game and setting up Zwane for an easy tap-in that the veteran winger gleefully put into the back of the net to secure his side a hard-fought victory.
Chiefs move up to fourth on 26 points, level with Orlando Pirates, while Thanda stay in 13th place on 19 points.