Ferrer looked to be in control of proceedings for much of the first set, frustrating Wawrinka and grabbing a break on the way to a 5-2 lead.
However, the Spaniard blew a set point in the ninth match and never truly recovered as Wawrinka, the number four seed, fought back to claim consecutive breaks while Ferrer's forehand and serve began to let him down.
Wawrinka's 7-5 victory in the opener was enough to seal Rafael Nadal's place in the last four, and the Swiss was soon on the verge of celebrating himself when he won the opening two games of the second set.
Ferrer's run of seven lost games in a row finally came to an end when he pulled it back to 2-1, but another break of serve in the fifth game put Wawrinka in complete control as he went in search of a fourth consecutive victory over the number seven seed.
There was one last show of defiance from Ferrer as he saved two match points, but it merely delayed the inevitable as Wawrinka served out the match to claim his first victory of the group stages.
Wawrinka will next take on Andy Murray in a straight shootout for a place in the semi-finals, while Ferrer can no longer qualify and faces Nadal in a dead-rubber on Friday.