Argentine champions Banfield slumped to a 2-0 home defeat against Uruguay's Nacional, their first loss of the competition, while Mexico's record scorer Jared Borgetti scored twice in Morelia's 2-1 win over Deportivo Cuenca.
Esteban Paredes took advantage of a catalogue of errors in the Velez defence to put Colo Colo ahead in the 57th minute at Santiago's Monumental stadium.
Velez, who became the first foreign team to play in Chile since a massive earthquake struck on Feb. 27, slipped deeper into trouble when Victor Zapata was sent off for a second bookable offence three minutes later.
However, Velez salvaged a point when Uruguayan forward Santiago Silva - who had a goal disallowed in the first half - scored from the edge of the area in the third minute of injury time, keeping his side at the top of Group Seven with seven points from three games.
"We played well but we were out of luck," said Paredes. "We had the points in our pockets."
Borgetti, 36, who has scored a record 46 goals for Mexico, was given a rare start by Morelia and responded with two first-half goals that gave his side their first win in Group Six.
The 'Desert Fox' headed Morelia in front from Elias Hernandez's cross in the 19th minute and fired the second from another Hernandez pass eight minutes later.
Jorge Ladines pulled one back for the Ecuadoreans - bottom of the group - in the second half.
Three-times winners Nacional overtook Banfield at the top of the same group with their win in Buenos Aires.
Sebastian Coates and Gonzalo Godoy scored twice in a 10-minute spell before half time to leave the Uruguayans with eight points, one ahead of their opponents. Morelia have four and Cuenca three.
Alianza Lima lost their 100 percent record in Group Three when they went down 4-2 at fellow Peruvians Juan Aurich.
Alianza still lead with nine points from four games, while Juan Aurich moved upto second with six, overtaking defending champions Estudiantes.
