The 9 teams were divided into 3 groups of 3 teams each. The teams played against each other on a home-and-away basis. The group winners would qualify. Brazil did not participate, as they were granted a spot in the finals after winning the 1962 World Cup.
Uruguay qualified.
Chile and Ecuador finished level on points, and a play-off on neutral ground was played to decide who would qualify.
Chile qualified.
Argentina qualified.
References
1966 FIFA World Cup qualification (CONMEBOL) Wikipedia(Text) CC BY-SA