Bolivia's Jhasmani Campos cancelled out Arturo Vidal's second-half opener when he scored an incredible free-kick midway through the second half at Gillette Stadium in Foxborough, Massachusetts.
But just as Bolivia looked to have taken a share of the spoils, the assistant referee called a controversial handball in the box to award a penalty against Luis Gutierrez in the eighth minute of stoppage time and Vidal made no mistake from the spot as he dispatched the winner for the defending champions in the 101st minute.
Juan Antonio Pizzi made three changes to the Chile side that lost 2-1 to Argentina in their Copa America opener last week as Mauricio Pinilla, Fabian Orellana and Pablo Hernandez came in for Eugenio Mena, Eduardo Vargas and Marcelo Diaz respectively.
Bolivia, meanwhile, were searching for their first win in seven games having lost their last six.
And they were unlucky to have Yasmani Duk ruled offside in the opening 10 minutes when he looked to be onside and through one-on-one only to be denied by the linesman's flag as he bore down on goal.
Chile still dominated, however, with over 75 per cent of possession and in the 39th minute the Bolivia penalty area looked more like a battle field as their defenders made a number of scrambling blocks, the most impressive of which came from Zenteno who blocked a fierce Sanchez shot on the line, to deny Pizzi's side a deserved opener and ensure parity at half-time.
But parity did not last long in the second half as Vidal opened the scoring just a minute after the break, netting his first goal for Chile outside of South America having started a delightful move.
Pinilla was released by Vidal into the box and got his head up in time to cut the ball back into a dangerous area, with the latter sharp enough to pounce on, turning it into the back of the net courtesy of a simple finish.
But if anyone thought Chile would run away with the win after taking the lead, they were proven wrong when substitute Campos stood over a 61st-minute free-kick having just been introduced by coach Julio Baldivieso.
Campos strode to the ball confidently and dispatched an incredible shot that looked to be going well wide before curling in and finding the back of the net via the cross bar as Claudio Bravo was left helpless.
Sanchez was turned away by a brilliant save from Carlos Lampe in the 72nd minute but the Chileans were not to be denied in contentious circumstances as Vidal stepped up and converted a penalty in the 11th minute of stoppage time after Gutierrez was adjudged to have handled the ball inside the area, much to the anger of Bolivia.