The 35-year-old Paris St-Germain forward becomes the second player to reach the milestone after Cristiano Ronaldo.
He also has 99 international goals, with two coming in the World Cup final.
The Argentina captain scored an 89th-minute free-kick at the Monumental de Nunez Stadium in Buenos Aires to add to Thiago Almada’s opener 11 minutes earlier.
Messi will have the opportunity to score his 100th international goal when Argentina play Curacao on Tuesday.
Magical Messi
It is yet another milestone in an extraordinary career during which he has won almost every major trophy, including four Champions Leagues, 10 La Liga titles, the Copa America and, finally in December, the World Cup.
Established as one of the greatest players of all time, Messi has won the Ballon d’Or – awarded to the best player of the year in European football – a record seven times, twice more than Ronaldo.
The only major competition Messi has played in but failed to win so far is the French Cup.
Messi’s haul of 35 trophies with Barcelona, whom he joined at the age of 13, makes him the most decorated player in the Spanish club’s history and he unsurprisingly holds Barca’s all-time scoring and appearance (778) records.
He has also scored more goals (474) and provided more assists (192) than any player to have featured in La Liga and has the record for the most goals in a single season in the Spanish top flight – 50 in 37 games during 2011-12.
He has the most La Liga hat-tricks (36) and shares the record for the most trebles in a single season with Ronaldo, who also has eight.
While the Portugal forward remains the Champions League’s all-time top scorer with 140 goals, Messi – who has 129 – was the first player to register five goals in a match in the competition and his sequence of scoring in 18 consecutive years is also unmatched in the European club game’s elite tournament.
Messi is already Argentina’s most capped player (172) and is one away from a century of goals for his country. Gabriel Batistuta is second on the list with a distant 56 from 78 games.
Only Ronaldo (120) and Ali Daei, who scored 109 times for Iran between 1993 and 2006, have scored more men’s international goals