Nacional goalkeeper Aristides Florentin kept his side in the game with two magnificent point-blank saves, while Oscar Diaz saw his fine looping header ruled out for offside.
Diaz was denied two more goals for fouls after the break, but the hosts at the Estadio Ramon Aguilera Costas kept the pressure on and finally took the lead 18 minutes into the second half.
The 27-year-old Diaz was hauled down in the box, but he did not take the chance to hit the net for a fourth time, Koke instead converting from the penalty spot.
Nacional pushed for a late equaliser as they looked to usurp The Strongest at the top of the table. However, they were caught on the counter with just three minutes left, substitute Marco Lazage sealing the points for Blooming, who move up to ninth place.
There was further misery for Potosi residents, as the city's other top-flight side, Real, also lost on Sunday, going down 1-0 at home to Club Universitario.
Mauricio Saucedo scored the only goal of the game five minutes after half-time as Universitario broke quickly from a Real corner and the 15-time Bolivia international crashed a left-footed effort into the top left-hand corner.
The win takes Universitario to seventh, seven points off a Copa Sudamerica spot, while Real are second from bottom with eight points from their opening 11 games.
