"The management has chosen Carlos Vicens, whose approach to the game, demands and emphasis on player development fully match the direction set by the club," Lyon said in a statement.
Vicens, 43, left SC Braga last month after 15 months in charge. He led the Portuguese side to the 2025-26 Europa League semi-finals.
He was part of Pep Guardiola's coaching staff at Manchester City from 2021 to 2025.
Vicens succeeds Fonseca, who left Lyon last week to become manager of Sporting.
Lyon sit fifth in Ligue 1 and 13th in the Europa League standings.