The 43-year-old former Rangers, Charlton and Finland striker has signed a two-year contract at Cappielow, where he began his coaching career back in 2012.
Chairman Crawford Rae told the club website: “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.”
Morton's next match is against Dundee United at Tannadice in the Ladbrokes Championship on Saturday September 15.