The complex formula used to determine the group standings meant Wawrinka knew that he only needed to win three games against the US Open champion to be guaranteed to finish as Group A runner-up.
Australian Open champion Wawrinka, who also made the last four at London's O2 Arena last year, wasted little time taking three of the first four games and, assuming he doesn't suffer a serious injury in the remainder of the Cilic match, he will play Group B winner Federer in Saturday's second semifinal.
The Lausanne native struggled, however, against Cilic as the match on Friday night went to three sets.
Wawrinka won the first set 6-3 before losing the second 4-6 to the Croatian, with the third set still undecided at 11pm Swiss time.
World number Novak Djokovic, who finished top of Group A, takes on Japan's Kei Nishikori, the Group B runner-up on his maiden Tour Finals appearance, in the first semifinal.