Malema, clad in his party's trade-mark red overalls, was ejected from the chamber after he refused to withdraw his comments, saying "I will never apologize to Cyril".
Malema and his party accuse Ramaphosa of having a hand in the 2012 killing of 34 striking miners who were gunned down by police near the Marikana mine operated by platinum producer Lonmin.
Ramaphosa was a director at Lonmin at the time and was cleared by a nearly three-year inquiry into what became known as the "Marikana massacre".
House chairwoman Mmatlala Grace Boroto ruled that Malema's remarks were derogatory and asked him to leave.
Malema refused, prompting her to call the Seargant at Arms to remove him, causing a brief scuffle around the EFF benches as Malema was pulled away by security guards.
Ten other people were killed in Marikana violence, including two police officers who were hacked to death.
The shootings led to intense public and media criticism towards the police, mining companies, unions and the ruling African National Congress.
Malema, who previously headed the youth league of the ruling African National Congress, has disrupted parliament before.
He and members of his party were removed by force after disrupting President Jacob Zuma's annual address in February.
At the time, Malema was demanding to be allowed to ask the president about when he would repay part of a $23 million state-funded security upgrade of his rural home. Zuma denies any wrongdoing.
South Africa's usually calm parliament has been shaken-up by the EFF winning 25 seats in last year's election. EFF members sport red overalls and hard hats in the chamber in a symbol of their solidarity the working classes.