The 22-year-old beat the London record time of 2:05:15 set by compatriot Martin Lel, last year´s winner, who withdrew on Saturday because of a hip injury.
Meanwhile defending champion Irina Mikitenko of Germany won the women´s race in a time of 2:22:11.
Wanjiru led home the first three from the Beijing Games, although in this race the minor placings were reversed, with the trio all finishing in personal best times.
Ethiopia´s Tsegaye Kebede, the bronze medalist in China, was second in 2:05:20 after pushing Wanjiru hard all the way while Morocco´s Jaouad Gharib finished in third in 2:05:27.
After a trio of pacemakers had set off at a blistering early speed, it had seemed as if Ethiopian distance running great´s Haile Gebrselassie´s world record time of 2:03:59 set in Berlin in September was under threat.
But hopes of a new world record started to fade at around the halfway mark.
"I get the course record but my target was the world record. The last 10km was very hard because I ran alone," Wanjiru, who made a series of bursts to stay ahead of Kebede, told the BBC afterwards having broken clear of the pack at 19 miles.
The 36-year-old Mikitenko, unable to run in Beijing because of injury, produced a dominant display.
However, it was not until some six miles from the end that she finally saw off the challenge of Mara Yamauchi, Britain´s standard-bearer in the absence of injured world record holder Paula Radcliffe.
"I was always confident that I had it in my legs as everything in myself felt good and after 19 miles I saw no reason why I shouldn´t win," said Mikitenko, after a third win in her fourth ´big city´ marathon.
Mikitenko´s two powerful surges late on proved too much for Yamauchi, who came in a personal best time of 2:23:12, having finished sixth in Beijing.
That left Yamauchi well clear of well clear of Russia´s Liliya Shobukova, who was third in 2:24:24.
Beijing champion Constantina Dita fell of the pace very early on while China´s Zhou Chunxiu, the Olympic bronze medallist and 2007 London champion, was dropped by the top two before the 17 mile-mark.
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