He appeared to have been taken through a different entrance to the rest of the public as he was not spotted in the main queue.
This raised the ire of EFF supporter Kutlwam Motloba, from Rustenburg.
“I wanted to see him (Malema). I felt we had the right to see him. Why did they hide him? The ANC knows they are going to lose,” he said, when news spread that Malema had arrived.
Earlier, the Economic Freedom Fighters leader visited Mandela’s house in Houghton with a group of fellow political supporters.
“Thank you [Mandela] for ushering in political freedom…. Those who came after you failed to deliver economic freedom,” he said.
“We are picking up this battle…Viva the militant Nelson Mandela, viva,” shouted the ousted ANC Youth League leader.
Members of the fledgling political party then laid red roses at a growing wall of tributes near Mandela’s house.
Long queues of thousands of people waiting for hours in blistering heat at park-and-ride facilities to get to the Union Buildings marked the second day in which Mandela’s body has laid in state.
At the seat of government, the mood was sombre as people filed past Mandela’s coffin, some saluting, others bowing their heads and some even gently waving, as they caught their last glimpse of the former president.
His coffin will be placed to lie in state for the third and last time on Friday.
The global statesman died at his home in Houghton, Johannesburg, last Thursday at the age of 95 after a long battle with a recurring lung infection.
He will be buried in a state funeral in the rural area of Qunu in the Eastern Cape in which he spent much of his childhood.