The Bavarians' coach struggled to hold back tears after his side's final Bundesliga game of the season, which they won 4-3 in dramatic style against Borussia Monchengladbach
Three goals in the first 10 minutes gave the hosts a head of steam but the Bavarians fought back with a goal from Javi Martinez, two from Franck Ribery and a winner from Arjen Robben to finish their record-breaking league season in dramatic style.
The win ensured that they top the Bundesliga by a massive 25 points ahead of second-placed Borussia Dortmund and Heynckes thanked die Roten's and Gladbach supporters alike for their send-off on Saturday.
"My thanks go to the fans for this wonderful farewell, which shows me ..." he began, before needing a moment to compose himself. "It shows me that this is my home.
"This is an emotional moment for me. I started my playing career and coaching career at Gladbach. It would certainly have been more emotional if it had been at the Bokelberg [Gladbach's old stadium].
"I associate many triumphs, bitter defeats and some curiosities with it. I would like to heartily thank the Borussia fans for the wonderful farewell."
Bayern will now prepare for their Champions League final against Borussia Dortmund on May 25 at Wembley.
A week later will be Heynckes' last game as Bayern head coach - the DFB-Pokal final against Stuttgart.