First-half strikes from Terry Antonis and Sasa Ognenovski saw Arnold's side prevail to move top on goal difference, with Adelaide United also on 10 points.
Arnold was coach at the Mariners for more than three years, but was celebrating a goal against them when Antonis fired home from long distance after 21 minutes.
It took just five minutes for Ognenovski to double Sydney's lead, albeit in fortuitous circumstances.
Milos Dimitrijevic's effort struck Ognenovski and wrong-footed Mariners goalkeeper Matthew Nash to roll in at the near post.
The visitors' woes were compounded when Mitchell Duke missed a late penalty, leaving them to dwell on a second consecutive loss.
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