The Austrian defender appears likely to join Real Madrid in the coming weeks, having run down his contract at Bayern.
He announced in February that he would be departing at the end of the season, and the reality of that decision has now dawned for Alaba.
The versatile player, who can perform at left-back and centre-back and has also featured in a defensive midfield role for Bayern, broke down in tears recently when watching a series of video messages prepared for him.
He posted a farewell note on Instagram, having wrapped up his Bayern career by helping the team to a 5-2 win over Augsburg on Saturday. Alaba, Javi Martinez and Jerome Boateng all featured for the final time.
Alaba's note on Sunday read: "My friends, my home, my love, all my pride. 13 years full of emotions, hard work, dedication, big moments, outstanding memories and love for the FC Bayern family.
"A time that taught me important lessons, that strengthened me and that made me the person who I am now. Season after season I learned what #MiaSanMia meant."
The club motto translates as "We are who we are", and is held in great reverence at Bayern.
"And every game I gave my best to show that. For you," Alaba added. "I will never forget, how we fought together on the pitch, celebrated our titles off the pitch and I will never forget how you, our fans, pushed and motivated us."
Alaba made 298 Bundesliga appearances for Bayern, scoring 24 goals and having 25 assists.
He helped the team keep 111 clean sheets across those games, did not receive a single red card in the league, and made only two errors leading to goals in the competition, according to Opta data.
Bayern team-mate Thomas Muller is the only other player in Bundesliga history to have won 10 titles, and Bayern have counted on Alaba as their Mr Dependable, the club stating he never served a suspension for accrued yellow cards in the league.
"I am glad and thankful that I could start here as a young boy with lots of dreams and that I could make these dreams reality," Alaba said. "Coming to Munich, joining FC Bayern was one of the best decisions in my life. Leaving this club and this city will be one of the hardest steps of my life.
"One thing for sure: I will never forget this time. @fcbayern"