Girona came into the match as the heavy favourite after its first leg victory, and immediately went back on the attack, creating serious problems for the Almeria defence again inside the first 10 minutes.
That fast start set the tone for a match in which Almeria never looked good enough to score, let alone find the goals it needed to progress to the final.
After a goalless first 45 minutes, the hosts, which made seven changes from the first leg, thought they had scored early in the second half when a free-kick was met by the head of Samuel Costa, but the ball was somehow saved on the line by Juan Carlos in the Girona goal, and there was also doubt about whether Costa had been offside.
That was as good as it got for Almeria, which will have to play second-tier football again next season in Spain, while Girona goes through to another attempt at promotion to LaLiga via the play-offs in the final, where it will play either Rayo Vallecano or Leganes on 21 June (AEST).
Like Almeria, Leganes will be looking to overturn a 3-0 first-leg deficit when it meets Rayo Vallecano in the second leg of their tie on Monday (AEST), with the winner going through to the final against Girona, and a shot at Spain's top flight.