Messi, who had dramatically announced the end of his international career in June following Argentina's Copa America Centenario final defeat to Chile, scored via a deflected shot in the 42nd minute to spark wild celebrations in Mendoza's Estadio Malvinas.
The victory -- the first under the reign of new coach Edgardo Bauza -- catapulted Argentina into first place in South America's marathon round-robin qualifying campaign with 14 points after seven games.
But Argentina was made to work hard for the victory, playing the second half with only 10 men after young Juventus striker Paulo Dybala was sent off just before half-time after a second yellow card. Dybala was led off the field in tears following the dismissal.
Yet with the talismanic Messi back in the fold, it was Argentina who enjoyed the better of the opening half.
Angel Di Maria created the first chance after 32 minutes, winning the ball brilliantly in midfield before laying off to Dybala who advanced on goal.
The 22-year-old let fly with a vicious low shot which crashed off the bottom of the post and cannoned into the back of diving Uruguay goalkeeper Fernando Muslera for a corner.
With half-time approaching Messi, pounced. A sublime piece of control took him towards the edge of the area, and his firm low shot deflected off of Jose Gimenez to deceive Muslera at the near post.
But Argentina's celebrations were cut short when Dybala saw red for a clumsy challenge on Mathias Corujo that drew a second yellow from Chilean referee Julio Bascunan.
That left Argentina needing to dig deep during a physical second half.
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