Jose Munoz scored for the second straight game as San Jose won for the third time in five Apertura matches.
It saw them jump into second spot on 10 points, the same number as league leaders Bolivar.
Nacional Potosi sit eighth on six points, with every team in the league having played five matches.
Munoz's 65th-minute goal was all that separated the teams at the Estadio Jesus Bermudez in Oruro as Miguel Zahzu's men claimed an important win.
San Jose visit Universitario Cobija on Sunday, while Nacional Potosi travel to Oriente Petrolero on the same day.
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