The prize, which comes on the same day the pair were named on the Ballon d’Or shortlist, was one of two picked up by the Argentine star, as Barca and Real Madrid all but swept the board.
Having guided Barca to the treble in his debut season in charge the club, Luis Enrique was named coach of the year, while two of his star forwards were also recognised.
Messi picked up the Best Striker award in addition to his Best Player gong, winning both for the sixth time, with team-mate Neymar – the third man on the Ballon d’Or shortlist – claiming Best American Player.
“It is a source of pride for me to receive this award [Best Player] ahead of of so many important players in the league, I’m very happy,” said Messi.
“This award, in particular, I want to dedicate to my son Thiago, even if he does not fully understand yet.”
Valencia’s Algerian midfielder Sofiane Feghouli picked up the Best African Player prize, while Barca’s Claudio Bravo was named Best Goalkeeper.
Ronaldo had to settle for the Fans’ Five Star Player award, with Madrid captain Sergio Ramos named Best Defender and the Best Midfielder award going to Colombian team-mate James Rodriguez.
Prior to receiving his award, and having accepted Ronaldo’s on the forward’s behalf, Ramos issued a warning to rivals Barca following their recent 4-0 Clasico success at the Santiago Bernabeu.
“It was a tough week after a negative result, losing a Clasico in that manner was a tough one to take,” he told Teledeporte.
“Now it’s time to forget all that and avoid dropping any more points in La Liga. Barca should enjoy this as much as they can, nothing lasts forever.”
In the second tier, Sporting Gijon’s Ivan Cuellar was named Best Goalkeeper, while colleague Bernardo Espinosa picked up the same award in the defenders’ category.
Valladolid midfielder Oscar Gonzalez and Real Betis striker Ruben Castro were honoured, as was Pablo Machin – coach of Girona.