Pratto shot low past goalkeeper Enrique Bologna at the Centenario, one of toughest venues in South America, in the 86th minute to put the Argentine champions level with their Uruguayan rivals on six points in Group Four.
The start of the match was marred by rival fans throwing objects at each other on the terraces with the police having to intervene forming a wide barrier between them.
"We read the game very well. They pressed and we defended well, then when we had the ball, above all in the second half, we played a very good match," Velez midfielder Federico Insua said.
Velez's victory, which puts them level with five-times champions Penarol on six points from three matches, came at a price with Argentina midfielder Fernando Gago coming off after half an hour with an injury.
Ecuador's Emelec, who have three points from two matches, are away to Deportes Iquique of Chile in the same group on Wednesday.