Lauener, who is also the chief executive of the Education Funding Agency (EFA), is due to start his role at the SFA on Monday 3 November.
He will retain his post at the EFA and will have separate accountability for each agency’s budgets.
Skills minister Nick Boles announced: “I am pleased to welcome Peter to his new post. He brings a wealth of experience in skills and in working with employers.
“In his new role leading both SFA and EFA he will join up our programme of reform across the education and skills sector.”
Lauener replaces Barbara Spicer who left the role after completing a nine-month contract in September.
He said: “I am delighted to take on this role and am looking forward to the challenge of making a difference in the skills sector.
“I have a long-standing interest and commitment to apprenticeships and skills and am keen to be involved in the next stage of reform.”