The Broncos needed to better Salford's result at Batley to keep their hopes of a Super League return alive, but the Red Devils won 42-14 to finish fifth.
Rhys Williams scored three of London's nine tries against Featherstone, who lost all seven games in the Qualifiers.
Both clubs will play in the Championship again in 2017.
London Broncos thrashed Featherstone in their final Qualifiers match but Salford's victory meant they missed out on a place in the Million Pound Game.