It had been expected that the former Barcelona boss would move to the Premier League next season, along with current Real Madrid boss Jose Mourinho.
"Heading home on the train catching up with today's news. I must say, I was surprised to hear that Pep Guardiola is going to manage Munich," Owen tweeted.
"Great club with a fantastic tradition but I thought if anybody was going to entice him back it would be Roman Abramovich. I was expecting Mourinho and Guardiola to both be managing in the Premier League next year."