The previous mark of 12:39.36 was set by fellow Ethiopian Haile Gebrselassie in Helsinki on June 13, 1998.
Trailing Bekele in second place was compatriot Mulugeta Wendimu, in a time of 13:01.28, with Kenya's Hillary Chenonge third in 13:08.77.
"It was very difficult," Bekele told Dutch public television after taking the lead in the fourth lap and then pulling away from the pack in the seventh.
"The pace was a little slow (at the beginning)."
Bekele, the world 10,000 metres champion, beat Gebrselassie over that distance at last August's Paris world championships.
He will contest the 10,000 metres event at a meeting in Ostrava, Czech Republic, on June 8.
"I haven't decided what to run at the Olympics and the results will help me determine that," the Ethiopian said earlier this year.
