ReutersClaudio Borghi's side will remain top until the next round of matches in September having overtaken Argentina, who had a bye on Saturday, which they spent beating World Cup hosts Brazil 4-3 in a friendly in New Jersey with a Lionel Messi hat-trick.
Chile have 12 points from six matches to Argentina's 10 from five and Copa America holders Uruguay, with eight points from four games, can move within a point of the new leaders if they beat Peru in Montevideo on Sunday.
The visiting team broke the deadlock with five minutes remaining when midfielder Matias Fernandez, the best player on the field, entered the box from the right and score with a shot that took a slight deflection.
With a tired Venezuela side looking for an equaliser, striker Charles Aranguiz scored from substitute Sebastian Pinto's cross to make the result safe for Chile one minute into added time.
Borghi dropped two players from his squad during the week after they were spotted at a Santiago nightclub only hours before the squad were due to resume training after a day off in Chile's second indiscipline scandal in seven months.
Despite the disruptions, Chile have won three qualifiers in a row, two of them on the road after last weekend's 2-0 victory in Bolivia.
Bolivia finally took full advantage of their high altitude home venue with a 3-1 victory over Paraguay.
The victory, Bolivia's first in six matches, lifted them off the bottom of the South American group standings with four points. Their only other success came with a surprise away draw in Argentina last year.
Paraguay, with one win in five matches, also have four points and could hit the bottom of the nine-team standings on Sunday if Peru, who have three points, avoid defeat to Uruguay in Montevideo.
Coach Francisco Arce's Paraguay side, who had a bye in last weekend's matches, had spent three weeks acclimatising for the match at the Hernando Siles, one of the world's highest football stadiums at 3,650 metres above sea level.
Arce's job could now be on the line, according to Paraguayan media, after he paid for his cautious tactics.
Bolivia benefited from the return from suspension of their Brazil-based striker Marcelo Martins, who played a key role in two of their goals although he did not score.
Striker Alcides Pena put Bolivia ahead in the 11th minute and Paraguayan-born midfielder Pablo Escobar scored twice in 10 minutes late in the second half to secure the points after Paraguay's goalkeeper Justo Villar had saved a penalty by Gualberto Mojica.
Cristian Riveros pulled one back for 2010 World Cup quarter-finalists nine minutes from time.
