The bodies of the couple, reported missing since February 23, were found in a canal near Udumalpet in the district, police said.
Passers by noticed the car in the canal and informed police, who rushed to the spot with rescue personnel and lifted the vehicle out.
Police suspect that the couple, in their twenties, might have consumed poison before driving down the canal as there was foam around their mouths.
However the man's family reportedly backed out after some time, which might have led them to take the extreme step, police said.