The statement said that Macron, in his call with Spanish Prime Minister Mariano Rajoy, expressed "his attachment to the constitutional unity of Spain."
The call came one day after the country's semiautonomous Catalonia region held a contested independence referendum that Spain's constitutional court had ruled illegal and unconstitutional.
Macron made no mention of the weekend violence in Catalonia, where national police were deployed to stop the vote from taking place. Some officers used rubber bullets and tear gas to disperse crowds and shut down polling stations, while protestors threw projectiles in response.
Catalan authorities said that hundreds were injured in the clashes. The Spanish Interior Ministry reported that a dozen police officers were hurt.
Catalan President Carles Puigdemont declared Sunday that the region had "won the right to an independent state", with roughly 90 percent of voters supporting secession from Spain.
However, only 42 percent of eligible voters participated in the banned independence referendum, according to Catalan authorities.
The European Union has called for dialogue between Madrid and Barcelona following the referendum violence.
Apart from Sunday's contested vote, Macron also discussed his ambitious EU reform plans with Rajoy, emphasising "the importance of close Franco-Spanish cooperation."