After a barren draw in the first half, Ayub Timbe broke the deadlock with less than twenty minutes to stoppage time but the host Nation restored parity towards the tail end though Rainford Kalaba.
Stars finished last in Group E with five points after one win, two draws and three loses. Guinea Bissau finished on top with ten points.
In related news, the wait is over as Uganda Cranes qualified for the 2017 Africa Cup of Nations with a one nil win over Comoros.
It is the first time Uganda will be taking part in AFCON since 1978. Other which teams which booked a place in next year’s tournament include Tunisia, Togo, Burkina Faso and Democratic Republic of Congo.
Sixteen teams will compete at next year's tournament, which runs from 14th of January to 5th of February. The sixteen teams are the 13 group winners and two best group runners-up, plus hosts Gabon.
Meanwhile, England started life under Sam Allardyce with a one nil win over Slovakia in their first match of the 2018 World cup qualifiers.
Adam Lallana’s scored in the final stages of the match as the unconvincing three lions secured all the three points.
Slovakia were forced to play the better part of second half with ten men after Martin Skirtel was sent off for a reckless tackle. Elsewhere, Thomas Muller scored a brace as world champions Germany beat Norway three nil.