Kljestan opened the scoring in the 29th minute after Felipe's cross split two defenders and Bradley Wright-Phillips' pass fell to Kljestan's feet for a tap in.
New York doubled the lead six minutes later when Lloyd Sam's cross found an unmarked Grella at the far post for an easy finish.
The Red Bulls moved into first place in the Eastern Conference and is one of two teams without a loss this season. Luis Robles made two big saves in the 83rd and 84th minutes.
San Jose conceded the first goal in its fourth straight away game. It hasn't won at New York during the regular season since 2005.
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