Ferrer sealed a routine victory over Andrea Seppi, romping through the match 6-1 6-4.
Wawrinka met a sterner adversary in Paolo Carreno, but having shared the first two sets came through to win 6-3 3-6 6-1.
Fans in Munich will be treated to an all-German final, as veteran Tommy Haas joined Philipp Kohlschreiber in winning his last-four match.
Munich Open men's quarter-final results:
4-Philipp Kohlschreiber (Germany) beat Daniel Brands (Germany) 6-7(4) 6-3 7-6(5)
3-Tommy Haas (Germany) beat Ivan Dodig (Croatia) 6-4 6-3
Oeiras Open men's quarterfinal results:
1-David Ferrer (Spain) beat 3-Andreas Seppi (Italy) 6-1 6-4
2-Stanislas Wawrinka (Switzerland) beat Pablo Carreno (Spain) 6-3 3-6 6-1