The Leagues Cup champion Columbus Crew also had two selections with forward Cucho Hernandez and MLS Defender of the Year Steven Moreira.
The Best XI is voted on by media members, MLS players and club technical staffs. The 2024 squad includes players from eight countries and nine teams and features seven first-time honorees.
Golden Boot winner Christian Benteke of DC United and Los Angeles FC's Denis Bouanga join Messi and Hernandez in the four forwards selected.
The three midfielders are Luciano Acosta of FC Cincinnati, Evander of the Portland Timbers and Riqui Puig from the Los Angeles Galaxy.
Seattle Sounders defender Yeimar Gomez Andrade joins Alba and Moreira on the back line, while MLS Goalkeeper of the Year Kristijan Kahlina is the first-ever Best XI honoree for Charlotte FC.
It was the fourth selection for Acosta and the second selection each for Bouanga, Hernandez and Yeimar.