The manufacturer had appealed to the European Court of First Instance against three Competition Commission fines given for a variety of alleged offences.
The court upheld a £7m charge, which Mercedes was given for its efforts to keep discounts on the E-Class to no more than 3% off the list price. Under competition rules, manufacturers are not allowed to dictate to dealers how much cars are sold for.
However, it was absolved of two anti-competitive practices. The court waived a £32m fine, which had been handed out by the commission for telling German dealers to demand 15% deposits from buyers from other countries.
It also overturned a £10 million penalty imposed on Mercedes for preventing dealers from establishing stocks of cars.