Dr Bloomfield announced his resignation in April this year.
Deputy Public Service Commissioner Helene Quilter said Dr Sarfati will take over the position on July 30.
"Dr Sarfati has considerable experience and a sound understanding of New Zealand's health system and has strong relationships across the sector," Quilter said in a statement.
Dr Sarfati is currently the head of Te Aho o Te Kahu, the Cancer Control Agency.
A recruitment process for a permanent director-general of health is underway and the role will advertise shortly, Quilter said.
The director-general of health leads the Ministry of Health which is the Government's chief advisor on health matters, a Public Service Commission statement announcing the appointment said.
Alongside chief executives of Health New Zealand and the Māori Health Authority, the director-general of health will lead the ministry and wider sector through the Covid-19 pandemic and upcoming changes to the health system, the statement said.
