Malema arrived two hours after the voting station opened in his hometown.
Earlier, EFF and ANC supporters had a verbal altercation after ANC members set up a tent and distributed T-shirts bearing the face of President Jacob Zuma.
EFF members accused the ANC of lobbying for votes at the voting station.
Police and IEC officials intervened and the matter was resolved.
EFF member Josi Buthane expressed disappointment at the Electoral Commission of SA (IEC), saying the electoral body was not enforcing the IEC regulations properly.
He said they should have stopped ANC members from distributing T-shirts at the polling station.
There was a heavy police presence in the area.
Malema’s party is contesting the election for the first time.
Some analysts in Limpopo believe the EFF could take seats currently occupied by other opposition parties in the provincial legislature.
Malema was head of the ANC Youth League until he was expelled from the ANC. All voting stations should be open from 07:00 and close at 21:00.