Werlé received the rank of "Chef de Brigade" on 25 March 1799 and promoted to "Général de Brigade" on 29 August 1803. He commanded a brigade in Jean-Baptiste Drouet, Comte d'Erlon's division of Marshal Jean-Baptiste Bernadotte's I Corps at the Battle of Austerlitz. Still serving as an I Corps brigadier, he played a role in the Battle of Schleiz on 9 October 1806, clearing a forest of Prussian outposts. He participated in the pursuit of the Prussian Army after Emperor Napoleon's army defeated it at the Battle of Jena–Auerstedt. He participated in the defeat of Duke Eugen of Württemberg's corps at the Battle of Halle on 17 October. Later, he was in on the defeat and capture of Gebhard Leberecht von Blücher's column in the Battle of Lübeck on 6 November.