His side won every game from the quarter finals onwards, including a late 2-1 win over league rivals Borussia Dortmund in the final at Wembley.
And Bayern have the chance to win their sixth consecutive Bundesliga title this weekend after dominating all season.
A 5-0 victory in last month's first leg in Munich had put Bayern in a commanding position and there was never any sign of a miraculous comeback in Istanbul on Wednesday.
The German side went ahead through Thiago Alcantara in the 18th minute with the Spaniard volleying in a Thomas Mueller cross to kill off any lingering hopes of a miracle recovery by the Turkish team after Bayern had crushed them 5-0 in the first leg in Munich.
Bayern Munich have won their last five Champions League games, the longest current run in the competition.
But Muller created a fine goal for Thiago to get Bayern up and running, the midfielder timing his run into the box perfectly to tuck away a first-time finish from a pinpoint right-wing cross.
But Bayern notched their third of the evening when back-up striker Sandro Wagner came off the bench to mark his Champions League debut with his first goal at this level.
Gonul started the second half with an own goal, minutes before a cat on the sideline caused referee Michael Oliver to halt the game briefly.
An innocuous right-wing cross from Rafinha should have been easy to clear, but Gonul poked the ball past Zengin under no pressure whatsoever. To date, he has reached the final of all three Champions League campaigns he has taken charge of, and no manager has ever made four consecutive finals.
Thiago broke the deadlock with a simple tap-in from Muller's perfectly weighted cross, quelling Besiktas' early energy with his second Champions League goal of the season.