Diego Forlan put Uruguay in front with a left-footed shot from 12 metres after a superb through ball by midfielder Alvaro Pereira left the striker alone with only goalkeeper Renny Vega to beat in the 39th minute.
With five minutes remaining, a header by Venezuela striker Jose Rondon was deflected into his own net by Godin with keeper Fernando Muslera wrong-footed.
Uruguay have gone five World Cup qualifiers without beating Venezuela, having lost 3-0 at home in 2004 and drawn the next four.
The result opened the way for Argentina to go top of the South American group if they beat Ecuador in Buenos Aires later on Saturday.
Copa America holders Uruguay and Venezuela, known as the 'Vinotinto' (red wine) for their burgundy strip, have eight points apiece and Argentina seven.
Uruguay captain Diego Lugano received a booking in the second half for a foul on midfielder Juan Arango and, since he was already on one yellow card, will miss the game with Peru at the Centenario on June 10.
The victory put Chile top of the South American group for two hours at least pending Argentina's meeting with Ecuador in Buenos Aires, while Bolivia remain rooted to the bottom with one point from five matches.
It was Chile third successive qualifying win at one of the world's highest football stadiums, the Hernando Siles which stands 3,650 metres above sea level in La Paz.
Chile weathered Bolivian pressure and took the lead in the third minute of first-half added time when young striker Charles Aranguiz scored his first goal for his country.
Midfielder Arturo Vidal, back in the side after he had his suspension for breaking a team curfew before a qualifier against Uruguay in November reduced, sealed the win seven minutes from time.
Frustration after failing to put away first-half chances crept into the Bolivians' game from early in the second with defender Luis Gutierrez sent off in the 52nd minute and four team mates booked in the next 20 minutes.
Bolivia sorely missed injured Brazil-based striker Marcelo Martins while Chile goalkeeper Claudio Bravo did well to keep a clean sheet.