If Atem had Kuriboh when Yugi attacked with Silent Magician, the attack would have been negated and the duel would have continued. Here's a potential way the duel could have continued (and with subtitles now)

I realized that the other video I originally posted had none of the subtitles of what Yugi and Atem were saying in their duel. Hopefully, this clears up what they were doing in their subsequent turns.