The 26-year-old American finished fifth in the second semi-final in 10.05 seconds while his Jamaican rivals, world record holder Usain Bolt and Asafa Powell, cruised through to the final as heat winners.
Jamaican Usain Bolt, the world record holder, was the fastest qualifier with a timing of 9.85.
Gay suffered a hamstring injury at the US trials last month and missed out on a place in the 200m, depriving him of a chance to repeat the sprint double he achieved at last year's world championships.
The final had long been expected to be a showdown between the three fastest men of all time, Bolt, Powell and Gay, but the two Jamaicans will now go head to head later on Saturday.