Apparently he passed a backmarker while under yellows. The cars lined behind Safety car were Hakkinen, Fissichella (1 lap down; can't remember, could be Wurz as Mr V said, but a Benetton anyway) and Schumacher. After the SC pulled out, apparently Schumacher passed (or at least he was not several car-lengths behind) Fissi, before the start-line.
The rules said that if the penalty was awarded with I don't know how many laps before the race ends, the penalty should be served in last lap. They gave him the stop and go with 2 laps to go. That is he entered the pits, but actually the line was before his box. It wouldn't count anyway, since he would have won that race even if he served the penalty and subsequently cross the line. The 25 seconds added at the total race time rule came after they saw what happened there.
Mr V is a bit wrong here. The technicality that he mentioned had the effect that the stewards completely dropped the penalty, several hours later.
(anyway, they were too late, they eventually handed Jean Todt the penalty, but it actually was a piece of handwritten paper, not the official form. It was rejected by Jean Todt, they came back with the proper form, and that caused even more delay)