Despite their defeat on Thursday, the Uruguayans head the pack as one of the three teams that lie neck and neck in the remaining automatic qualification places, just a point behind the leaders.
The other two are Colombia, who got the better of Venezuela on Thursday, and Ecuador, in spite of their loss to Brazil.
Messi's deflected strike was enough for Argentina to scrape past Uruguay and make it five straight home wins over their neighbours in the World Cup preliminaries.
Messi finally got Argentina on the board after 42 minutes. After taking a nice touch to settle the ball at the top of the box, he shifted around and got an effort towards the goal that hit off Jose Gimenez and found the back of the net.
Argentina then managed to keep their historic rivals at bay despite being at a numerical disadvantage for the whole second half following Paulo Dybala's sending-off on the stroke of half-time.
