Morton secured promotion to the First Division despite collapsing to a two-goal defeat at Stark's Park.
Jim McInally's side dominated during a barren first half, but the Rovers managed to frustrate Morton.
The home side picked up two second-half goals in just six minutes through Todd Lumsden and Dennis McLauchlim.
Despite the defeat, the party started in Kirkcaldy for the champions because closest challengers Stirling Albion lost out at Ayr United.
Following the match, McInally spoke to BBC Scotland about his frustration at the loss.
"I'm delighted, believe it or not, but I'm just angry at the second-half performance," said McInally.
"We've had a fantastic season, and today was the first time I've seen the players' nerves go a bit."
On securing promotion to the First Division, McInally was cautious, but admitted that he would be seeking an improvement in Morton's performances.
"We'll need to play a lot better than that," he added.
Raith Rovers: Fahey, Wilson, Pelosi, Lumsden, Andrews, Fotheringham, Ian Davidson (Kilgannon 88), Bonar, Hislop (Silvestro 41), McLauchlim, Neill (Dingwall 82). Subs Not Used: Ellison, Mackie.
Booked: Lumsden, Fotheringham, Ian Davidson.
Goals: Lumsden 70, McLauchlim 76.
Morton: Mathers, Weatherson, Macgregor, Harding, Greacen, McLaughlin, Finlayson (Millar 59), Stevenson, Templeman (Linn 68), McGowan (Russell 77), McAlistair. Subs Not Used: McGurn, Walker.
Booked: McLaughlin.
Att: 4,327
Ref: Chris Boyle
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