Sergio Blanco and Santiago Garcia scored in each half to take Nacional one point ahead of Danubio, who had led the championship's first stage when the tournament was interrupted.
Wednesday's game was originally due to be staged in August but was called off by the referee because Nacional turned up several minutes late for the kick off.
Villa Espanola were awarded a 2-0 walkover win but Nacional appealed for a replay, arguing that games often start late in Uruguay, and the Uruguayan Football Association (AUF) ruled in their favour last week.
The ruling was criticised by Nacional's arch-rivals Penarol and the AUF also came under fire for taking so long to reach a decision.
The tournament was suspended on Nov. 17, a day after fans fought a vicious battle on the pitch following the top-of-the-table match between Danubio and Nacional, which Danubio won 1-0.
Shortly after the final whistle, Nacional fans broke down the fencing at the tiny Jardines del Hipodromo stadium and invaded the pitch. At one point, they managed to snatch a Danubio flag from home fans, who also invaded the field.
In the battle that followed, rival fans attacked each other with iron bars and used the corner flags as weapons.
The suspension was lifted on Tuesday after the AUF and the Ministry of the Interior agreed on new security measures.
These included moving high-risk games to the Centenario stadium, the installation of metal detectors and closed-circuit cameras and breathalyser tests to identify drunken fans.
The championship was also suspended for several weeks in 2006 after a Cerro fan was stabbed to death in front of his wife and children by supporters of rivals Penarol near the Centenario stadium.
Uruguay won the 1930 and 1950 World Cups but, due to economic problems and a small population, have been unable to keep their status as a major power.
Although the country still produces an impressive number of players for export, there has been a more dramatic decline at domestic level.
Many first division games are played in stadiums that resemble European non-league grounds and in front of tiny crowds.
