In July 1871 he was returned to the National Assembly for Marseille at a by-election, and voted steadily with the Republican party.

At the general elections of 1881, after the fall of the Jules Ferry cabinet he was returned to the chamber on a programme which included the separation of Church and State, a policy of decentralization, and the imposition of an income tax.

Rouvier's opposition in his capacity of president of the Budget Commission was one of the causes of the defeat of Charles Floquet's cabinet in February 1889.

Accusations that he accepted bribes from Cornelius Herz and the baron de Reinach compelled his resignation from the Ribot cabinet during the Panama scandals in December 1892.

Under a law passed in April 1905, for instance, a certain credit was earmarked in the French budget for the purpose of public subsidies for unemployment benefit funds.

At a cabinet meeting on 5 June Rouvier reproached the Foreign Minister with imprudence over Morocco, and after a heated discussion Delcassé resigned.

Lengthy discussions resulted in a new convention in September, which contained the programme of the proposed conference, and in December Rouvier was able to make a statement about the whole proceedings in the chamber, which received the assent of all parties.

The disturbances arising in connection with the Separation Law were skillfully handled by Georges Clemenceau to discredit the ministry, which gave place to a cabinet under the direction of Sarrien.