SARS spokesman Sandile Memela confirmed the resignation to TimesLIVE.
Sources close to the matter say Matlwa tendered his resignation on Wednesday after he was served with a suspension letter.
It is not clear what the suspension related to.
Memela would not go into the details of the resignation, saying: “SARS does not divulge or discuss its employees and related matters between employee and employer in the public domain.”
He returned to SARS in 2015 as CFO during Commissioner Tom Moyane’s restructuring process.
Memela said Johnston Makhubu, who is the current SARS group executive for procurement, will be the acting CFO.
“SARS wishes to assert that the organization has a capable and skilled leadership and employees that work as a collective to fulfil its mandate. SARS has for two consecutive years, collected over a R1-trillion. With this in mind, the organization remains resolute, focused and single-minded about meeting our revenue collection target of R 1.265-trillion,” he said.