The British-Brazilian duo were beaten by South Africa's Raven Klaasen and American Rajeev Ram 6-1 6-4 in an hour at the O2 Arena in London.
But Murray and Soares have already overtaken Pierre-Hugues Herbert and Nicolas Mahut in the year-end rankings.
After three round-robin match wins, they were outplayed by Klaasen and Ram.
The latter pair will play Finland's Henri Kontinen and Murray's former partner, Australian John Peers, in Sunday's final.
Kontinen and Peers beat the Bryan brothers 7-6 (7-2) 6-4 in their semi-final.
Earlier, Jamie's brother Andy Murray kept his hopes alive of ending the season as the world number one singles player by beating Milos Raonic in a thrilling semi-final, which lasted three hours and 38 minutes.
New world number one doubles team Jamie Murray and Bruno Soares suffered a disappointing defeat in the semi-finals of the ATP World Tour Finals.