The 44-year old guided Killie into the top five before departing Rugby Park to take the Finland national team job about a month ago.
Paatelainen said he was humbled to win the award and thanked his players and staff for their efforts throughout the campaign.
"There have been some famous names who have picked up this trophy before and to be in that list is a great honour," he said.
"This season there have been loads of fantastic managers in the SPL and I'm over the moon to win this.
"We have had a great season at Kilmarnock. We were relegation candidates at the start of the season and we qualified for the top six comfortably and there was even a chance of getting into Europe.
"It's been a really, really positive and enjoyable season because of the players' work rate, their effort and their receptiveness."