Bartomeu was arrested on Monday alongside several other people as part of a police investigation into their alleged involvement in the 'Barcagate' smear campaign scandal.
Guardiola, who spent 17 years at Barcelona as a player and four as a manager, hopes the club's new president will help them move on from the difficult state of affairs surrounding them at present.
The Manchester City boss said: "I know it's an uncomfortable situation and hopefully it is going to finish well. He's already now innocent until the court maybe proves he is guilty.
"The only thing I'm concerned with right now is that in one week we'll have a new president. I want to congratulate all three for the campaign.
"Of course it's a difficult situation all around the world and at Barcelona especially for many reasons as everyone knows, so have the courage to lead the next years.
"Hopefully as many people as possible can vote and choose the right president to lead this incredible club, for me the best club in the world, for the sentimental issue.
"I'm pretty sure Barcelona will come back stronger in a short time. The new president just has to lead the confidence of everyone, and join the team and the fans all together and they are going to be the club they are.
"I'm looking forward to the election next Sunday and hopefully the president we choose will be OK."