With Messi watching from the stands, Malcom started and scored in the 1-1 Champions League draw.
Mundo Deportivo says Messi pushed for the Brazilian's selection in the lead up to the game after speaking with coach Ernesto Valverde.
The Argentine questioned Valverde about "whether there is a problem with Malcom?", which the coach insisted "no".
After the chat, Valverde decided to go with Malcom against Inter and was rewarded with a goalscoring performance.