The Ugandan received the accolade ahead of Masandawana teammate Khama Billiat and TP Mazembe's Rainford Kalaba.
Billiat, who was named runner-up, was widely tipped to claim the honour but Onyango was recognised for his feats between the sticks for the Brazilians as his 12 clean sheets helped them to a record-breaking league win last season.
Although injured early in the CAF Champions League final second-leg against Zamalek he was instrumental in getting his side to that stage with a clean sheet against the Egyptians in the first-leg, putting them in a good postion to go on and win the crown.
The 29-year-old shot-stopper was named 2015 Ugandan Player of the Year at an awards ceremony last year as well as being named PSL Goalkeeper of the Season.