Austria's Benjamin Raich, Renfried Herbst and Rainer Schoenfelder were 1-2-3 in the slalom, giving their country 14 medals in 10 alpine events.
It was the second gold for Raich, who won the giant slalom, and the second bronze for Schoenfelder.
Ligety, the surprise winner of the combined, recorded the third fastest time in the first run. Officials then disqualified him for straddling a gate.
Raich had a combined time of 1:43.14 while Herbst rallied from seventh place for a silver at 1:43.97. Schoenfelder was clocked in 1:44.15.
Kentaro Minagawa just missed what would have been the second alpine medal ever for Japan. He finished .03 of a second behind Schoenfelder.
The United States won only two alpine medals at these Olympics -- the same number Americans won in Salt Lake City.