Showrunner Jack Kenny previously announced the renewal on his Twitter feed, but later retracted his statement, claiming that he had "misconstrued a conversation" with Syfy executives.
Kenny has now signed a new deal to continue producing the show and develop new projects for the network.
"Jack Kenny's superlative leadership and the incredible talent of his cast and crew delivered an outstanding second season of Warehouse 13," said Syfy programming chief Mark Stern. "We're excited to see this successful series return next year and to be developing our next hit with Jack."
The second season of Warehouse 13 averaged 3.4m viewers, making it Syfy's most watched series this year.