Sandro Rosell resigned his post as president of the Catalan giants on Thursday, amid reports Spanish courts are to open investigations into the transfer of Neymar from Santos in the close-season.
The deal which was estimated to be in the region of €57 million has faced scrutiny following claims of a misappropriation of funds, with Spanish newspaper El Mundo Deportivo reporting to have seen documents showing the deal was closer to €95m.
Rosell refuted the claims and reaffirmed his stance that everything in the Neymar transfer was "correct", but decided to offer his "irrevocable resignation" at an emergency board meeting on Thursday, with Bartomeu assuming control for the remainder of his time in charge - which runs until 2016.
Bartomeu backed Rosell's stance and plans to fight the accusations, while paying tribute to the departing president.
Speaking at a press conference, he said: "We are going to be very, very strict in our defence of respect for our club against all of the sporting and judicial authorities.
"President Rosell, my friend, thank you for everything that you've done. We're very grateful to you. I'm so sorry you've had to present this resignation because you know you have all of our support.
"It's been an honour to work with you these years and there are memories I will treasure forever."
Bartomeu continued by thanking his fellow board members, and vowed to continue the recent success enjoyed by Barcelona.
He added: "My companions of the board, I thank you for the confidence to put me in control of this project for now. My first message as president of Barca is to announce that our mandate will continue until 2016.
"We feel strong, we were the most voted candidacy and we will continue to work for the values we've continued to observe for these last years, and we're excited and committed to maintaining the excellence in the three areas of our club, the sport, the economic area and the social area.
"All of our challenges are still as valid as ever, referring to the football team and the other sports teams, we will continue to support them with all the resources that they need to fight for everything."
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