Hoeness stepped down from his position as president and chairman of the club's supervisory board on Friday after he was sentenced to three and a half years in prison for tax evasion.
The 62-year-old was found guilty of seven counts of tax evasion, defrauding authorities of a total of €27.2 million.
Herbert Hainer, who had previously held the post of deputy chairman of the supervisory board, has been named as chairman until further notice.
But, ahead of Saturday's clash with Bayer Leverkusen, Guardiola insisted that he will remain friends with Hoeness.
"I've been only a few months here and I've seen how important Uli Hoeness is for this club," Guardiola said.
"Bayern is one of the best clubs in the world and that has been largely possible thanks to the character of Uli Hoeness.
"Uli deserves all our respect, he is and will remain my friend. Now we have to continue working as he taught us.
"We have to continue on our way, both Uli and the players know it, and now we have to concentrate in every game."
Bundesliga leaders Bayern host third-placed Leverkusen at the Allianz Arena as the defending champions seek to make it 50 league games unbeaten.
Leverkusen were the last side to beat the Bavarians in the league, earning a 2-1 away win back in October 2012.
And Guardiola feels Leverkusen, who were knocked out of the UEFA Champions League after a 6-1 aggregate loss to Paris Saint-Germain, will pose a threat to their undefeated streak this weekend.
"Leverkusen played very well in Paris, going 1-0 up (before losing 2-1). They are very organised defensively," Guardiola added.
"We will lose sooner or later, but we have to remain focused on retaining our title."
