Napoleon occupied Vienna before the Battle of Austerlitz.
French forces entered the Habsburg capital in November 1805 during Napoleon’s campaign against the Third Coalition. After defeating an Austrian army at Ulm, the Grande Armée pursued the retreating allies down the Danube and captured Vienna, gaining control of its bridges, arsenal, and major military supplies.
The occupation did not end the campaign. Austria remained in the war, and a Russo-Austrian army moved to confront Napoleon in Moravia. Napoleon then drew the allied army toward Austerlitz, where the two sides fought on 2 December 1805 in the Battle of the Three Emperors.
The French victory at Austerlitz was one of Napoleon’s greatest battlefield successes. It forced Austria to negotiate the Peace of Pressburg and helped destroy the Third Coalition. Vienna was occupied again by French forces in 1809, which can cause confusion when the city appears in accounts of multiple Napoleonic campaigns.
Munich and Prague were important regional cities, but neither is the Austrian capital identified in this question.