Messi, with earnings of £82.9 million, occupies second spot behind Mayweather, with Ronaldo in third on £80.6m.
His move above Ronaldo comes after he signed a new contract at the Camp Nou, with Brazil star Neymar (£67.2m) now in fifth place following his world-record move from Barcelona to Paris Saint-Germain last summer.
Forbes said Messi's annual salary and bonus was more than £59m before tax, making him the year's highest-paid player, with endorsement deals with companies including Adidas and Pepsi adding to his fortune.
Ronaldo has a place in the list's top three for a sixth successive year, while Neymar has risen 13 places to fifth after putting pen to paper on a lucrative five-year contract with PSG.