In a statement on Saturday, ANC spokesperson Jackson Mthembu commended Finance Minister Pravin Gordhan for the "decisive action" he took in probing the allegations of impropriety and misconduct when they were initially levelled against Magashula.
"We respect [Magashula's] decision to relinquish his post in the face of controversy and place … the reputation and integrity of Sars [South African Revenue Service] and government broadly ahead of his own deployment interests," Mthembu said.
Gordhan previously ordered an investigation into allegations that Magashula offered a chartered accountant a job at Sars.
The investigation was conducted by retired justice Zak Yacoob and advocate Muzi Sikhakhane.
According to reports in March, Magashula allegedly offered a job to a chartered accountant in a recorded telephone conversation facilitated by a Timothy Marimuthu who allegedly had influence over Magashula.
Gordhan said the reports raised questions about the integrity of staff recruitment processes at Sars, and he had appointed Yacoob and Sikhakhane to investigate.
Ivan Pillay's appointment
Gordhan said on Friday he would instruct the Sars audit committee to investigate whether Magashula's behaviour breached any tax processes.
He would also appoint a committee to review Sars's governance and ethical standards, pertaining to the office of the commissioner.
Deputy commissioner Ivan Pillay was appointed acting commissioner until the appointment of a new head at Sars. – Sapa