Montanes, the fourth seed, raised his career finals record with 4-4 with the victory over the home crowd favorite. He downed world No. 1 Roger Federer in the semifinals to reach the championship round.
With the win, Montanes became the first back-to-back winner at Estoril since Thomas Muster took the event in 1995-96.
Gil, meanwhile, failed in his bid to win his first ATP title. He reached the final after outlasting fifth-seeded Guillermo Garcia-Lopez in the previous round.