Messi, 38, needed just seven minutes to reach his milestone, coolly tucking away a low finish to give Miami a 1-0 lead in the regional club competition knockout game.
The strike took Messi's tally to 81 goals for Miami following his move to Major League Soccer in 2023.
The eight-time Ballon D'Or winner previously scored 672 goals for Spanish giants Barcelona, 32 for France's Paris Saint-Germain, and a further 115 international goals for Argentina.
Messi's 900th goal comes some 21 years after his first goal in senior football, when he scored for Barcelona in a 2-0 win over Albacete in 2005.
Messi still has some way to go before he catches his great rival Cristiano Ronaldo, the 41-year-old Portuguese superstar who is on 965 career goals.
The Argentine World Cup winner's 900th goal came early in Miami's last-16 second leg tie with MLS rivals Nashville.
After a bright start by Miami, Messi collected a pass from left back Sergio Reguilon inside the penalty area, and duly slotted a clinical finish past Nashville goalkeeper Brian Schwake.
The goal put Miami 1-0 ahead on aggregrate as they bid to advance to the quarter-finals of the premier club competition for teams from North America, Central America and the Caribbean.