Malvern-born Killeen, suffered a suspected broken ankle after falling at the bottom of a steep section of boulders, named Deane's Drop.
The 30-year-old, who was fifth in Athens and seventh in Beijing, was the first of several high-profile riders whose race came to a premature end.
French rider Julien Absolon, the champion at both Athens and Beijing, also bowed out on the second lap after a puncture on the opening circuit saw him drop right back through the field.
The race was won by Jaroslav Kulhavy from the Czech Republic, who was one of three riders who had been together for much of the race. He edged ahead of Swiss rival Nino Schurter by just one second on the line.
The bronze medal went to Italy's Marco Aurelio Fontana, 25 seconds down after dropping back in the final 4km after his saddle fell off.