The reigning Asian champions have been in devastating form in the Asian Champions League but have been unable to produce the same performances in the domestic competition.
With just one win from their last five encounters, Gamba have slipped to 6th on the table whilst Kobe have now won two on the trot and join Gamba on ten points.
Hiroto Mogi opened up the scoring for Kobe in the 11th minute before Gamba's Brazilian star Leandro equalised four minutes later.
From then on it was all Kobe who went ahead in the 26th minute through Mogi once again before Marcel round out the victory a minute from time.
It was a vital victory for Kobe over their Kansai rivals as a loss or draw would have placed them in the bottom five in the J-League.
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