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The Argentine star struck the decisive goal in the 83rd minute, lifting his Major League Soccer total to 26 for the campaign.
Messi won his first MLS Golden Boot last year, finishing with 29 goals from 28 appearances.
At 39, the eight-time Ballon d’Or recipient is in position to become the first player to capture the award in back-to-back seasons since MLS introduced its current format, based solely on goals scored, in 2005.
With one fixture left on the regular-season schedule, Messi has a strong chance to widen his lead over Musa and add another landmark achievement to his MLS record.