Wednesday's ruling also orders a freezing of assets for a former head of Petrobras and three members of its board of directors.
Court justice Vital do Rego said there were signs of "intentional mismanagement to cover up irregularities". The one-year freeze covers assets that could be used to recoup the loss.
Rousseff was board chair when the purchase was initiated in 2006. She said in a statement that there was "no evidence of illicit acts" and that she would appeal the ruling.
Rousseff was impeached and ousted as president last year for violating fiscal management rules.