According to Vic Lombardi of CBS Denver, Thomas suffered a separated shoulder in the first quarter.
That was on 2nd and 7 with the Seahawks leading 5-0 (Denver fumbled their first play from scrimmage that resulted in a Seattle safety and then minutes later a field goal).
There would be no shock involved if Thomas hurt himself on this play. Whatever the case, the star wideout suffered a tough injury to deal with. Staying healthy wouldn't have changed the outcome of the game, but it certainly didn't help the Broncos much.