Torres calmly stroked a 51st-minute spot kick down the middle with goalkeeper Romel Quinonez diving right to convert a penalty earned by Javi Martinez. (Agencies)
Spain controlled play at the Sanchez Pizjuan but found it hard to convert against a well-organized Bolivian team before Iniesta charged forward to curl around Quinonez in the 84th to seal victory.
Vicente del Bosque employed an experimental team, trying out different combinations with key Real Madrid and Atletico
Madrid players still missing following the Champions League final last week.
The Spain coach will announce his 23-man squad for next month's tournament on Saturday, with winger Jesus Navas likely to be omitted because of a long spell out to an ankle injury. Despite the goal, Torres made little impact up front and failed to soothe Spain's attacking worries with Diego Costa's status uncertain because of thigh muscle injury.
But the Chelsea striker looks certain to be in Brazil after stepping up to score his 37th goal for Spain in his first appearance since the Confederations Cup final loss to Brazil last July.
"I have a lot of confidence in Fernando Torres," Del Bosque said. "We're happy with his work."
While Juan Mata and Pedro Rodriguez managed scoring opportunities, it wasn't until the second-half entrances of Iniesta, Sergio Busquets and David Silva that Spain looked more capable of scoring, with Cesc Fabregas coming on to reprise his role as an unorthodox striker.
"We had an encouraging week of training and today was a positive day," said Iniesta, who fooled Quinonez with a shot the Bolivian goalie thought was set to land outside the far post.
Del Bosque said midfielder Ander Iturraspe and defender Alberto Moreno would not be in Brazil despite playing on Friday.
Spain, which opens Group B against the Netherlands on June 13, travels to the United States on Sunday ahead of its June 7 friendly against El Salvador in Washington. Spain also plays Chile and Australia in Brazil.
Torres calmly stroked a 51st-minute spot kick down the middle with goalkeeper Romel Quinonez diving right to convert a penalty earned by Javi Martinez.