FNB announced on Wednesday Jordaan will be replaced by Jacques Celliers, who is currently the chief executive of FNB Business Banking.
Speculation that Jordaan wanted to resign began in January with reports that his imminent resignation was linked to the fallout over FNB's controversial ad campaign, "You can help". Jordaan denied this at the time.
The campaign featured video clips of school children criticising the government. In one of these, a school child referred to Basic Education Minister Angie Motshekga as "brainless".
The clips went viral, provoking a fiery response from the ANC and the ANC Youth League, which called the adverts "treasonous".
FNB reportedly apologised to the ANC for the furore.
Handing over the reins
​On Wednesday, FirstRand's board said Jordaan first announced his intention to resign in 2010.
"He was comfortable that having been chief executive for 10 years he would have achieved the strategic and operational objectives that he set out for the business at the beginning of his tenure," the board said.
It said Jordaan would hand over the reins to Celliers incrementally over the next six months, in what is expected to be "smooth" transition. Jordaan said he was sad to leave FNB, but that the bank was in "great shape".
"Recently voted the most innovative bank in the world and with a clear leadership position in digital banking and innovative banking channels, FNB will continue with its successful strategy of generating new technologies and cost-effective products for our customers," he said.
Sizwe Nxasana, chief executive of FirstRand, said that Jordaan had overseen a period of significant business growth, innovation and profitability at FNB and was an individual with exceptional skills and experience.
"Michael's tenure at FNB has been incredibly successful. Much of which can be attributed to his passion for innovation which, backed up by his knowledge of the intersection of banking, technology and social media, has delivered strong growth and excellent returns for the group and its shareholders," Nxasana said.