Shortly after winning the World Cup title with a 1-0 extra time victory over Argentina, Spaniards claimed all three individual player awards, keeping 39-year-old Messi from leaving with any more personal hardware.
Rodri won the Golden Ball as the tournament's best player, Unai Simón won the Golden Glove for the top performance by a goalkeeper, and Pau Cubarsí won the Best Young Player Award, beating out fellow 19-year-old teammate Lamine Yamal.
Argentina captain Messi was hoping to win a record-extending third Golden Ball as the tournament's best player.
He's already the only player to win the award multiple times since it was first given in 1978, and sparking Argentina's run to a second straight final at age 39 gave him a strong case for another.
But the award went to Rodri after he captained Spain's run to their second World Cup title.
The Manchester City midfielder didn't have a goal in the tournament, but his passing and controlling the possession are central to the way Spain plays. He became just the 11th man to win the World Cup, the UEFA Champions League and Ballon d'Or.
Simón set a record with his seven shutouts in the tournament, allowing just one goal in eight games.
The 27-year-old Mbappé totaled 10 goals and four assists for a France team that finished fourth. Messi ended up with eight goals and four assists after going without a goal or an assist on Sunday for the first time in his last 12 World Cup games.
The Golden Boot is one of the few things Messi has never won in his storied career - he was second to Mbappe in 2022 - but he went into the final weekend with the lead. Both Messi and Mbappé had eight goals through the semi-finals, but Messi owned the tiebreaker with one more assist.
Mbappé then scored two goals and had an assist on Saturday in France's 6-4 loss to England in the third-place game, making him the first player with 10 goals in a World Cup since Germany great Gerd Müller had 10 in 1970.
Mbappé has 22 career World Cup goals, one better than Messi for the tournament record.