Maximiliano Olivera grabbed the all-important goal in the 54th minute to send Wanderers to their first Torneo Final since 1985.
Wanderers have not been crowned Uruguayan champions since 1931 when the top flight remained an amateur competition.
However, a seven-game winning run has propelled them to the top and they will now face Apertura winners Danubio for the championship.
The duo's presence in the showpiece means Uruguay will have a champion other than the giant pairing of Nacional and Penarol for the first time since 2008-09.
Penarol stumbled last week against Liverpool to hand Wanderers the initiative and the favour they needed to top the table did not arrive, despite doing their bit with a 3-1 win over Cerro Largo.
Defeat for Cerro Largo was their ninth in 10 games and leaves them at the bottom with just nine points to their name.
One place and one point above them finished Miramar Misiones - who drew 2-2 with Juventud.
Six defeats in the Clausura campaign wrecked Nacional's hopes of the title, but they ended the season on a high with a 4-1 win at Fenix.
Danubio's Joao Alves finished up the Clausura's equal top corer with nine goals, but heroics came from elsewhere as his team-mates came from three goals down to draw 3-3 at home to Sud America.
Racing, River Plate and Cerro each rounded off their campaigns with wins over Rentistas, Defensor Sporting and Liverpool.
