The former Rangers striker and coach takes over from Ray McKinnon who controversially walked out on the club last week to join Championship rivals Falkirk.
Johansson, 43, has signed a two-year contract.
It is a first manager’s job for the former Finnish international who won over 100 caps for his country.
He had a spell on the coaching staff at Morton in 2012 before moving to Motherwell. He was then part of the Finland management team before returning to the Scottish game as assistant coach to Pedro Caixinha at Rangers.
Morton chairman Crawford Rae told the club’s website: “We are absolutely delighted to announce Jonatan Johansson as the new manager of Greenock Morton Football Club.
“Jonatan has a fantastic CV, both playing and coaching, and has been eager for an opportunity to get into management. We are thrilled about our appointment and we look forward to sharing this new chapter together.
“JJ has a fantastic work ethic, a great football brain, and I cannot wait to see him in action as we rekindle Greenock Morton’s long-standing Nordic association of over 50 years.”