Supersport United were the defending champions, having won their first Premiership title on the final day of the previous season.
Bloemfontein Celtic survived relegation on goal difference, ending 14th on the league table with 33 points.
It was the second time that the Orlando Pirates midfielder bagged the coveted Footballer of the Year honour, following his controversial win last season.
This time, however, Modise's brilliance from the unusual left of midfield position helped Pirates mount a championship bid.
Ajax Cape Town's Franklin Cale won the award for the Telkom Knockout Player of the Tournament.