The Frenchwoman, who is the current world-champion in the event, pulled out on the 80th lap, having cycled nearly 27 kilometres in 33min 46sec.
Britain's Yvonne MacGregor holds the current world record of 47.411km set in Manchester last June.
Longo was trailing Macgregor's mark when she retired from the velodrome, averaging 47.385kmh compared to 47.411kmh.
1. France 167 points 2. Germany 152 3. Denmark 124 4. Australia 123 5. Italy 123 6. France Espoirs 106 7. USA 76 8. Spain 61