First off, the defender was already on a yellow card, so a second yellow would get him sent off. Second, the fact that it's stoppage time is completely irrelevant. What happens is that, with the ball at the defender's feet, he kicks it in the air and then heads back to the goalie. This, according to the rules, means a yellow card.
http://en.wikipedia.org/wiki/Back-pass_rule
"As the rule specifically requires that the pass be done with intention and through a kick, an infraction would not occur if a player uses their head, chest or knee to make the pass nor would it be an infraction if a keeper recovers a ball that was merely last touched by a team mate. It would however be an infraction if a player was to use a deliberate trick to pass the ball to their goalkeeper, such as kicking the ball up and then using their head. If a player were to use such a deliberate trick then they must be issued a caution."