The Brazilian international was charged with four alleged breaches of FA rules in relation to matches involving the Premier League side.
It was alleged that the 27-year-old directly sought to influence matches by intentionally seeking to receive a card from the referee for the "improper purpose of affecting the betting market".
He denied the charges and the independent regulatory commission found the charges not proven following a hearing.
The Football Association said two charges against Paqueta related to a failure to cooperate with its investigation had been found proven.
It said a commission would decide on an appropriate sanction for those proven breaches "at the earliest opportunity".
The Brazilian said in a statement issued by West Ham that he had always maintained his "innocence against these extremely serious accusations".
West Ham United vice-chair Karren Brady said: "We are pleased Lucas has been cleared. He has maintained his innocence from the outset, and as a club we have resolutely stood by him and supported him throughout the process."