He says his decision is "a rejection of hate" rather than a rejection of South Africans.
France is yet to comment on Yann Vezilier's pardon and previously called the accusations "unfounded".
The army says it was involved in fierce fighting but disputes that Islamists took control of the garrison.
The ship carried armoured personnel carriers and trucks through the English Channel to Africa, satellite images show.
The blockade has led to shortages of fuel and food ahead of next week's Muslim holiday of Eid.
The death toll is unclear but sources say between 30 and 50 people died in Wednesday’s attacks.
Former Defence Minister Sadio Camara was killed in a massive offensive by combined jihadist and separatist forces.
The blockade comes days after Mali's defence minister was assassinated in a series of nationwide attacks.
The UK has issued similar advice, telling citizens who stay, that they do so at their own risk.
