Fellow Brazilian striker Kleber also scored two for Cruzeiro in their 2-2 draw at Venezuela's Deportivo Italia in Group Seven but was sent off near the end for a bad tackle, his second yellow card offence.
In two Group Five matches played in Ecuador, modest Uruguayan side Cerro shocked Emelec 2-1 in the George Capwell stadium in Guayaquil while Ecuadorean champions Deportivo Quito were held 1-1 by Brazil's Internacional in the capital.
Washington, who also scored both goals in Sao Paulo's 2-0 home win over Mexican champions Monterrey a month ago, took his tally in South America's top club competition to four.
"Of course, against Once Caldas I had that chance, I didn't take it and the team lost," Washington was quoted as saying on Brazilian broadcaster Globo's sports website.
"But there are going to be lots of games when I'm not going to score and the team will lose. No one's unbeatable and no one's perfect. But also, many times, I'll settle (the game), like today," he said.
Washington opened the scoring with a left-foot shot against the run of play just before the hour and tapped in a cross in the final minute of the match, played in front of less than a thousand spectators at Asuncion's Defensores del Chaco stadium.
Kleber was sent off five minutes from time and Italia's substitute left back Rafael Lobo was shown a straight red card in the 89th, two minutes after coming on.
In Guayaquil, Cerro midfielder Pablo Caballero put his side in front early in the second half when he tapped in the rebound after Alvaro Melo's shot had hit the bar.
