Jones suffered a hamstring injury last week and did not play Sunday against the Indianapolis Colts. He returned to practice on Tuesday.
In a statement issued through the team, coach Mike Singletary said, "I'd like to thank Brandon for the effort he put forth during his time with the 49ers. Letting Brandon go at this point will allow him the opportunity to latch on with another team. We wish him all the best in the future."
Jones, 28, was signed last year as an unrestricted free agent after playing his first four seasons with the Tennessee Titans. He appeared in eight games for the Niners last season and caught one pass for 18 yards.
With Jones gone, Dominique Zeigler, Jason Hill and Kyle Williams appear in competition for the team's last two wide receiver spots. Zeigler has been the most impressive in camp, and Williams is out for about two weeks with an injury to his big toe.
Patrick, who has been out with a shoulder injury, was signed last October from the Kansas City Chiefs and played in three games.