The midfielder finished just 242 votes clear of the Ecuadorian, with the big Swedish striker finishing a close third.
Among the highlights of the season for the Herrera were a goal and an assist in a 2-0 win over Chelsea last month.
Herrera is the second successive Spaniard to win the award after his compatriot David de Gea took home the prize last season.
While the midfielder claimed the club's top award, right-back Valencia was voted the Man United Players' Player of the Season.
Henrikh Mkhitaryan was the winner for the club's Goal of the Season award for his superb effort against Sunderland, and 16-year-old Angel Gomes became the youngest ever winner of the club's Youth Team Player of the Year award, while Axel Tuanzebe collected the Reserve Player of the Year gong.