The 62-year-old stepped down on Friday and after being sentenced to three-and-a-half-years in prison for tax fraud.
Guardiola said: "Today it is not easy for me. I've only been here nine months. I wish my German was better so I couldexpress my feelings more clearly. I've noticed in this short time how important Uli Hoeness is to this club.
"The club is one of the largest in the world. That would not have been possible without him. He deserves all of our respect. In the short period I have been working incredibly with him. I hope he can come back in the future and support us. "After being initially charged with evading €3.5 million in taxes, Hoeness eventually acknowledged hiding €27.2m from the German authorities and was sentenced on Thursday.
Although his defence team claimed the 62-year-old would appeal, Hoeness has insisted he will accept the conviction and immediately relinquished his responsibilities as Bayern chief ahead of his incarceration.
"After discussions with my family, I have decided to accept the judgement of the District Court of Munich regarding my tax conviction," he said in a personal statement released on Bayern's website on Friday.
"I have instructed my lawyers not to appeal. This corresponds to my understanding of decency and personal responsibility.
"Tax evasion was a mistake in my life. The consequences of this error I must implement myself.
"In addition, I resign with immediate effect my duties as president and chairman of Bayern Munich. I want to avoid causing harm for my club.
"Bayern Munich's my life's work and it will always be there. I'm going to stay connected with this great club and its people in many other ways, as long as I live.
"To my personal friends and supporters of Bayern Munich, I thank you from the bottom of my heart for your support."
Bayern later released a statement, in which they acknowledged Hoeness’ decision to stand down and thanked him for his service to the club.
It read: “Uli Hoeness has today informed the Supervisory Board of Bayern Munich in a personal statement that he has with immediate effect resigned his positions as president of FC Bayern Munich and the chairman of FC Bayern Munich AG.
“The Supervisory Board has noted this with the utmost respect.
“The entire Supervisory Board of Bayern Munich would like to thank Uli Hoeness for his extraordinary achievements for the benefit of the club over the past four decades.”
Herbert Hainer, who steps up from Hoeness’ deputy to chair the Supervisory Board until further notice, added: “Uli Hoeness has always served with leadership, personal dedication and outstanding lifetime dedication to the benefit of FC Bayern Munich.
“He is largely responsible for making sure that FC Bayern Munich has become one of the most athletic and economically successful and attractive clubs in the world.
“For that, thank you.”