Freiburg opened the scoring in just 12 minutes through Japanese international Yuito Suzuki, who finished a perfect close-range effort.
The club has requested the written justification of the ruling from UEFA to appeal the decision.
Vincent Kompany’s side were confirmed champions on Sunday without even kicking a ball.
Bayern continued their onslaught after the break, and Olise teed up Kane for a shot from the edge of the box, which led to the striker’s 41st Bundesliga goal.
“I’m looking forward to the challenge of FC Bayern,” Kompany told Bayern Munich’s official website.
Both teams forced each other’s goalkeepers into a couple of saves in the game’s opening minutes.
City are currently on three consecutive EPL title wins and seek to become the first EPL club to win four consecutive league titles.
Free-scoring Super Eagles prospect, Chuba Akpom, scored Middlesbrough’s only goal from the spot. It was his 26th league goal of the season as he leads the top scorers’ chart.
Kompany will take over from Mike Jackson who replaced Sean Dyche in April but could not rescue the clube from relegation.
