The Inter Miami star took his international goal tally to 106 with strikes in the 32nd and 42nd minutes at Lima’s Estadio Nacional.
Messi’s first-half brace left reigning world champions Argentina on top of the South American qualifying table with 12 points from four games, five points clear of Uruguay, Brazil and Venezuela, who all have seven points.
Restored to the starting line-up after coming off the bench in last Thursday’s 1-0 win over Paraguay, Messi showed no sign of the injuries that have recently limited his appearances in Major League Soccer.
The 36-year-old crashed home an emphatic opener just after the half-hour mark, then added a second 10 minutes later after good work by Enzo Fernandez down the left flank.
The win leaves Argentina firmly on track to return to the World Cup finals in 2026, which are being expanded to include 48 teams and will be co-hosted by the United States, Mexico and Canada.
The top six teams in South America’s 10-team qualifying competition will be guaranteed a place at the finals.
While Argentina continued their serene progress through qualifying, arch-rivals Brazil suffered a nightmare 2-0 defeat in Montevideo, crashing to a first loss against Uruguay in 22 years.
The defeat was compounded by the sight of veteran forward Neymar being stretchered off just before half-time with what appeared to be a knee injury.
Uruguay’s Darwin Nunez struck with a bullet header on 42 minutes to open the scoring in a dour first half at the Estadio Centenario.
The Liverpool striker then played a pivotal role in Uruguay’s second, holding up the ball well from a throw-in and cutting back for Nicolas de la Cruz to fire past Brazil goalkeeper Ederson on 77 minutes, sealing a 2-0 victory.
The win was Uruguay’s first over Brazil in a World Cup qualifying fixture since a 1-0 victory over the Selecao in Montevideo in July 2001.
The defeat marked another disappointing result for five-time world champions Brazil, who were held to a 1-1 draw by Venezuela last week in the previous round.
Brazilian team officials said Neymar would undergo examinations in Sao Paulo on Wednesday to assess the nature of his injury.
Venezuela meanwhile boosted their hopes of reaching the World Cup for the first time with an impressive 3-0 rout of Chile in Maturin.
Winger Yeferson Soteldo was the star for La Vinotinto, scoring the opening goal and setting up second-half goals for veteran striker Salomon Rondon and Darwin Machis.
Soteldo opened the scoring in stoppage time at the end of the first half, stabbing a low angled shot into the bottom corner to the delight of a raucous home crowd.
The Santos winger turned provider for Venezuela’s second, bursting down the left flank and cutting back for Rondon to sweep home from close range on 72 minutes.
Soteldo was also involved in Venezuela’s third, once again finding space on the left wing and crossing for an unmarked Machis to make it 3-0.
Elsewhere Tuesday, Paraguay got their first win of the qualifiers, defeating lowly Bolivia 1-0 in Asuncion with a 69th-minute strike from Antonio Sanabria.
Bolivia remain bottom of the standings while Paraguay are seventh with three points from four games.
In Quito meanwhile, Colombia maintained their unbeaten start to qualifiers with a 0-0 draw away to Ecuador.
AFP