The Croat has taken a parting shot at the Bavarian giants' coach, claiming that he made a tactical error against Chelsea and also slamming him for his selection policies
The Bavarians netted an 83rd-minute goal through Thomas Muller, who was then substituted for an additional defender. Shortly after, Didier Drogba equalised for the Blues to take the game to extra time, and the English side eventually prevailed 4-3 on penalties at the Allianz Arena.
Pranjic feels that Heynckes was at fault for the defeat after altering the back line when they were in front.
"He changed the defence just before the end [of the Champions League final]. Daniel Van Buyten was brought on [for Muller] - that was a mistake," he said to Sport1.
"The defence looked good for 85 minutes, and he changed it!"
The 30-year-old then went on to criticise Heynckes' selection policy, stating that the veteran trainer alienated large sections of the squad.
The Croatia international featured intermittently under former coach Louis van Gaal, but since the former Real Madrid boss' advent at the Allianz Arena, has made just a handful of appearances.
"Last season was really hard for me," he confessed. "Heynckes was new to Bayern and didn't include me in his plans.
"It was difficult, not just for me, but for all of the other players, and finding the right motivation was tough."
Pranjic, who has confirmed that he received an offer from a Chinese club, is currently at Euro 2012 with Croatia, and although he went on to state that he was pleased with his country's opening match, a 3-1 win over Republic of Ireland, he was wary of facing Italy, who began their campaign with a 1-1 draw against Spain.
"Obviously it's a shame that I wasn't on the pitch, but the team played well and we deserved to win. Quite frankly [Italy] have surprised me against Spain. Italy are once again a good team."
Croatia lock horns with Cesare Prandelli's men at 18:00CET on Thursday.