Johannesburg - Henry Okah was convicted on 13 charges of terrorist activities by the High Court in Johannesburg on Monday.
"I have come to the conclusion that the State proved beyond reasonable doubt the guilt of the accused," Judge Neels Claassen said when handing down judgment.
"The evidence of all the accomplices that worked with him was not contradicted... I found that [Okah is the] leader, planner, funder, supplier... of car bombs used in Warri in March 2010 and on October 1 2010."
Claassen said Okah's failure to testify meant evidence against him remained uncontested.
Twelve people were killed and 36 injured in the car bombs on 1 October 2010, the anniversary of Nigeria's independence. Okah was arrested in Johannesburg the next day.
He was also found guilty on terrorism charges relating to two explosions in March 2010 in the southern Nigerian city of Warri.
Claassen found no evidence that Okah did not head the Movement for the Emancipation of the Niger Delta, which claimed responsibility for the blasts.
He was found guilty of engaging in terrorist activities, conspiracy to engage in terrorist activity, and delivering, placing, and detonating an explosive device.
About 34 witnesses were called during the trial.
Okah denied any involvement in the blasts and said the charges against him were politically motivated.
South Africa tried him as part of its international obligation, as the Nigerian authorities had not applied for his extradition, according to the prosecution.
National Prosecuting Authority spokesperson Phindi Louw said the State had "a watertight case against Okah".
The case proved great results could be achieved if law enforcement agencies worked together, Louw said.
State prosecutor Shaun Abrahams said justice had been done. The ruling showed South African and foreign law enforcement agencies could work together.
"There is no safe haven in South Africa."
Abrahams said legislation provided for a minimum sentence of life imprisonment for Okah's crimes.
After the guilty finding, Okah was taken to the court holding cells under heavy police guard.
When his wife became emotional, a friend comforted her. They then left the courtroom.
About 10 police officers were in the court, with another four outside while the case was being heard. The main road in front of the court was also closed.
Sentencing procedures were expected to start on 31 January.