The international anti-piracy agreement was signed by the European Commission and 22 EU member states in January but never officially ratified.
Since then, many countries backpedaled on their decision to sign following widespread protests that followed.
The proposed agreement is regularly compared to stalled US legislation SOPA. It seeks to establish international standards for intellectual property rights enforcement.
However, opponents suggest it impinges on civil liberties and freedom of expression.
Today's rejection vote arrived despite an attempt to postpone the decision because of ongoing investigations into the agreement by the European Court of Justice.
A total of 478 MEPs voted against the deal, with 39 in favour. There were 165 abstentions.