The Barcelona star opened the scoring after 15 minutes of play with his 33rd goal for the Albiceleste, before equalling Maradona on 34 when he converted a spot kick shortly before the half-time whistle.
His second-half goal made it 4-0 to Argentina and saw him overtake the 52-year-old in the all-time goalscoring charts with his 35th strike.
Nevertheless, Messi has remained calm following his latest achievement and has downplayed the significance of surpassing Maradona.
"Having overtaken Maradona is not important. The main thing was to end this friendly well as a team, which isn't easy ahead of the holidays," the forward told reporters.
Messi's hat-trick saw him move to joint second spot in the Argentina goalscoring charts alongside Hernan Crespo, but he still has a long way to go if he is to become the national team's all-time leading goalscorer as Gabriel Batistuta sits atop with 56 goals.