Two goals from striker Agustin Delgado kept Ecuador going well in CONMEBOL's 2002 World Cup qualifying.
They now have ten points and are level with Chile and just one point behind Brazil.
The Necaxa striker scored with a header in the 18th minute from a cross by Ulises de la Cruz and hit a low drive in the 61st minute but an earlier handball in the move saw some Bolivian protests.
The visitng team needed Ecuador to pay their travel and hotel costs to play this fixture after recent money problems for the Bolivian federation.
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