Defending champion Athanasia Tsoumeleka of Greece could only manage a 9th-placed finish in 1:27.54.
Kaniskina got a boost close to the 10km mark when Tatyana Kalmykova, Russia's national champion and one of the main challengers, was disqualified for not making contact with the ground.
|Heavy rains played havoc with Thursday's Olympic schedule [GALLO/GETTY]
China's Yang Mingxia, who had also been seen as a potential medalist, was also disqualified.
With torrential rains drenching Beijing on Thursday morning, several scheduled Olympic events were delayed or postponed by a day, but the walk went ahead as planned although raincoat-clad officials had to battle to sweep water from the track.
Despite the rain, the stadium was nearly full.
Men's javelin qualifying groups were delayed by more than an hour, and at least two throwers slipped and fell as officials used towels to try to soak up puddles of water on the runway.
Women's high jump qualifiers and the decathlon long jump and shot put were also delayed by more than an hour.
Both the BMX semi-finals and final were postponed until Friday.