Malema's suspension from the African National Congress (ANC) comes into immediate effect, the party's national disciplinary committee said in a statement.
Malema had already been suspended from membership of the party in November but was still allowed to attend party meetings while the appeals process was in progress.
Malema's appeal against the disciplinary committee's ruling will be heard on April 12.
The latest sanction from the disciplinary panel follows a speech Malema made Friday in which he suggested that Zuma was running the party in a dictatorial and intolerant way.
"It is under President Zuma that we have seen the youth of the ANC being traumatized, being expelled from their own home," Malema said, according to the ANC statement.
"It is under President Zuma we have seen a critical voice being suppressed. We have seen under President Zuma, democracy being replaced with dictatorship."
The disciplinary panel said the youth leader's remarks constituted "a very serious violation" of the party's constitution.
Malema attracts wide popular support and his suspension may cause anger among his base.
He and the youth league helped propel Zuma to power in 2009, but have more recently become his fiercest critics, accusing his administration of failing to improve the lives of the poor.
The party is due to elect a new leader in December this year, who will likely lead the party into national elections in 2014. Malema has previously been mentioned as a potential contender for the role.
Malema was suspended for five years after the disciplinary hearing last November but was allowed to appeal.
He faced a string of charges, including sowing party divisions by comparing Zuma to his predecessor, Thabo Mbeki, and bringing the party into disrepute by urging the toppling of the Botswana government.
In July, Malema criticized South Africa's decision to vote for a no-fly zone over Libya and accused the government of failing to prioritize the African agenda.
"In the past, we know President Mbeki used to represent that agenda very well," Malema was quoted as saying at the time.
Malema's supporters considered the disciplinary action an attempt to silence the anti-Zuma voice within the ruling party.
Malema has also been the subject of a criminal investigation by the national revenue service over allegations he used his political position to influence the awarding of government tenders.
