João Sousa, who is ranked 68 in the world, beat his namesake, who is ranked 143th, for the fourth time in four encounters. The score was 4-6, 7-6 (7-1), 7-5, in a match that lasted two hours and 26 minutes.
The Portuguese number one is now to face the UK's Kyle Edmund, who is seeded third in the competition, in what will be the two players' third encounter. So far, each has won one match.
João Sousa last reached the quarter-finals of the Estoril Open in 2012 - before the organisation of the Estoril Open changed hands in 2015 and when it was still in the grounds of the National Stadium, at Jamor.