The visitors did what they could in the hope of a Dunfermline stumble in the play-off race thanks to a George Oakley first-half double and a Nathan Austin strike in the second, but they finished fifth with the Greenock side two places further down.
Morton announced before kick-off that long-serving chairman Douglas Rae was stepping down due to ill-health and was being replaced by his son Crawford. The new chief got down to work yesterday by parting company with Duffy, pictured, who still had a year of his contract left.
The former Falkirk, Dundee, Hibs, Brechin City and Clyde manager took over at Morton four years ago just after they had been relegated to League 1.
Within a year Morton were promoted as champions. They have scompeted in the promotion play-offs as well as reaching the Betfred Cup semi-finals last season.
A club statement read: “We would like to thank Jim for his hard work and commitment to the club over the course of his four seasons here at Cappielow and wish him the very best of luck in his future career.
“The board of directors will now focus on identifying and recruiting the right person to take Morton forward.”
Dunfermline swatted visitors Dumbarton aside 4-0 to secure the last play-off place, the Pars starting their second shot at promotion against Dundee United on Tuesday night.
The Sons, who will try to secure another season of Championship football by defeating Arbroath and then either Raith Rovers or Alloa in the play-offs, made a terrible start, with Craig Barr dismissed after only nine minutes for a crunching challenge on Andy Ryan.
Kallum Higginbotham volleyed Dunfermline ahead on 18 minutes before clipping in the second from a tight angle seven minutes later. Fraser Aird added the third from an even tighter angle and Ryan Williamson poked in the fourth on 65 minutes to set up the double-header against a Tannadice side that Dunfermline have not defeated in 13 attempts.
Manager Allan Johnston said: “Those games are in the past now. It is all about what we do now that matters.”
Falkirk’s technical director Alex Smith bowed out after 60 years in Scottish football on a high after the Bairns defeated title-winners St Mirren 1-0. Ryan Blair hit the winner five minutes from time with a terrific strike from 25 yards.
Dundee United bounced back from their three-goal hammering at Queen of the South by defeating Livingston 2 – 0 at Tannadice. Craig Slater turned in a Billy King cross to open the scoring on 54 minutes and Scott McDonald’s close-range header five minutes from time sealed the win.
The season is ending too soon for Queen of the South who made it three wins in a row with a 5-1 win at Brechin who ended the season without one win. Stephen Dobbie hit a hat-trick and Lyndon Dykes a double as the Doonhamers led by five before Isaac Layne grabbed a consolation goal.