After achieving their first ever World Cup victory, the 'blue sharks' were unable to surprise Slovenia and lost 92-77, in a match in which they reached half-time leading 45-38.
Slovenian Luka Doncic had his least productive match at the World Cup, but even so, he finished with 19 points, seven rebounds and nine assists, with Benfica's Betinho Gomes being the best of the Cape Verdeans, with 17 points.
With three victories, Slovenia won Group F, ahead of Georgia, who defeated Venezuela (70-59) and also secured passage to the next stage, with Cape Verde in third place and the South Americans in fourth.
In the matches between 17th and 32nd place, Cape Verde will face Finland on Thursday, with the other Portuguese-speaking African country in the competition, Angola, playing China.
Brazil secured passage to the next stage, with an 89-77 victory over Ivory Coast, with whom they were fighting for second place in Group G, which had Spain already as the winners.
Yago Santos was the great figure of the match, with 24 points, 12 assists and four rebounds.
Spain ensured a perfect first phase, beating Iran, last in the pool, 85-65, with Juancho Hernangómez being the top scorer, with 21 points.
The United States, big favorites for the final victory, also ended the first phase with plenty of triumphs, after clearly defeating Jordan, 110-62, with Anthony Edwards (22 points and eight rebounds) in the spotlight.
In Group C, the North Americans finished with six points, one more than Greece, which secured qualification with a victory over New Zealand (83-74), third placed, with Jordan in last place.
Also with a perfect record, Serbia won Group B, after beating South Sudan, 115-83, and will be accompanied in the second phase by Puerto Rico, who defeated China, 107-89.