The ruling African National Congress (ANC) took Johannesburg with 44.55 percent of the votes, final results showed on Saturday.
The opposition Democratic Alliance (DA) won 38.37 percent of the votes, and the Economic Freedom Fighters (EFF) 11.09 percent, the Independent Electoral Commission (IEC) announced.
With less than 50 percent of the votes, the ANC will have to form a coalition government with opposition parties.
The DA said it had succeeded in dragging the ANC below the 50 percent mark, which had never happened before.
The ANC suffered its biggest setback in the local government elections since 1994 when apartheid was brought to an end, losing the administrative capital of Tshwane (Pretoria) and the strategic Nelson Mandela Bay metro to the DA.
In Cape Town, the DA increased its share of the vote from 60.92 percent in 2011 to 67 percent in 2016.
Outside of the metros, the DA won 19 municipalities with an outright majority. They span three provinces, Gauteng, the Eastern Cape and the Western Cape.
The elections, seen by many as being the most contested since 1994, took place on Wednesday. For the first time in history, the elections saw 200 political parties and over 61,000 candidates participating to seek control of eight metros and more than 200 municipalities.
The number of registered voters stood at 26 million and voter turnout was at least 58 percent, the IEC said.
The ANC's nationwide support has declined from 61.9 percent in 2011 to 53.91 percent in 2016, while support for the DA has grown from 23.9 percent to 27 percent.
The local government elections "were hotly contested with competing parties passionately arguing their points of view to win over the electorate", President Jacob Zuma said on Saturday.
"That is how it should be in a democracy," Zuma said.
Source: NAM NEWS NETWORK