The Barcelona superstar, who has often failed to find top form for his country, set the pitch alight with his magnificent left foot, weaving through Nigeria's defence at will to deafening cheers at a three-quarter full stadium.
The trickster set up the first goal with a deft chip that sent Gonzalo Higuain clear in the 25th minute. Angel Di Maria tapped home the second two minutes later after Messi again ran through the gaping Nigerian defence before his shot was parried by the goalkeeper, the ball falling invitingly for Di Maria.
Nigeria were better in the second half, reducing the margin through an Obasi Chinedu goal on 46 minutes, but the Africans lost their way after conceding an own goal following a Higuain attempt.
Messi came close to scoring twice in the first half, sending the crowd to their feet as he dribbled past four Nigerian defenders before his left-footed shot to the far post was saved by the outstretched hands of Dele Aiyenugba. He again came close to scoring but his shot on the stroke of half-time was saved by the busy Nigerian keeper.
It was new Argentina coach Alejandro Sabella's second victory in as many matches. His team beat Venezuela 1-0 in the eastern Indian city of Kolkata on Friday. Sabella replaced Sergio Batista as coach in the wake of Argentina's disappointing performance at the Copa America on home soil in July.
The 14-time Copa winners were knocked out on penalties in the quarter-finals by Uruguay, triggering a wave of criticism from home fans desperate to see their team break an 18-year title drought.