Wanjiru's feat was even more remarkable given the strength of the opposition, as aside from 34-year-old Bekele there was Eritrean world champion Ghirmay Ghebreslassie and Ethiopia's Olympic silver medalist Feyisa Lilesa.
The 24-year-old Wanjiru came home in a time of 2hrs 5min 48sec to beat Bekele, who recovered from a poor patch mid-race to come roaring back in the final eight miles, but ultimately fell just short.
Bekele finished nine seconds adrift whilst Wanjiru's compatriot Bedan Karoki was third in 2hr 07:41.
Bekele, whose training was interrupted when he was ill three weeks ago, went through a bad patch and looked like he folded completely shortly after the halfway mark.
He dropped from the lead group but rediscovered some of his vim and trailed the leading three runners by eight seconds.
Wanjiru broke free to lead but Bekele was firmly into his stride and eating up ground, moving into second past a tiring Karoki, with the amateur runners coming down the opposite side of the road applauding the Ethiopian.
Bekele set off in pursuit of Wanjiru and in stark contrast to his downcast look earlier in the race, raised his arm in salute to a coterie of Ethiopian supporters as the race headed towards its climax.
Wanjiru, winner of the Amsterdam Marathon last year, started to cast anxious glances behind him as Bekele remorselessly ate into his lead, but the Kenyan still had a lead of around seven seconds with less than two miles to go.
The shock of seeing Bekele gaining on him appeared to refocus Wanjiru and he extended his lead late on.
He was sufficiently relaxed to raise his arms in celebration entering the final straight – before enveloping Bekele in a hug after the latter crossed the line.