Bolivar headed into Sunday's game with Nacional Potosi knowing a win would be enough to win the opening championship of the 2013-14 season.
However, Miguel Portugal's men fell at the final hurdle as a 42nd-minute goal from Ivan Huayhuata secured the points for Nacional.
That allowed The Strongest the opportunity to seal the title, and Eduardo Villegas' side made no mistake, cruising to their sixth league win in a row with a comfortable 3-0 victory over Real Potosi.
Goals from Diego Bejarano, Gabriel Rios and Jair Reinoso made sure of the points for The Strongest, enabling them to claim their 11th league crown and a place in the Copa Libertadores.
Third-placed San Jose rounded off their Apertura campaign with a 4-1 win over Guabira, while midfielder Roger Espinoza scored a hat-trick as Wilstermann hammered Oriente Petrolero 6-1 to finish fourth.
Elsewhere, Blooming beat bottom side Aurora 3-2, and Sport Boys played out a 0-0 draw with Club Universitario.
The Clausura season begins on January 18.
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