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The 24-year-old South African, a double amputee, missed his personal best by 0.08 seconds, clocking 45.69 in difficult conditions, running in lane one in persistent rain.
Pistorius charged down the finishing straight, holding off the likes of World Championships bronze medallist Renny Quow of Trinidad and Tobago, who finished seventh, and Continental Cup silver medallist Ricardo Chambers of Jamaica, who was eighth.
Jeremy Wariner of the US, the former world and Olympic champion, won in 45.13, finishing a little more than half a second ahead of the South African.
Pistorius clocked 45.61 in Pretoria in March, setting a lifetime best and reaching the B-qualifying standard of 45.70 -- a mark he bettered again in New York -- for the global championships in Daegu, South Korea in August.
His season's best fell 0.36 seconds short of the A-qualifying standard which would secure him a place in the national team.
Pistorius, who also hopes to qualify for the Olympic Games in London next year, is ranked fourth in South Africa in 2011, which puts him in contention for a place in the men's 4x400m relay squad for the global championships.
