The Olympic and world 10,000 metres champion held off a strong challenge from Kenya's Isaac Songok to cross the line in 10 minutes 54 seconds at Fukuoka's chilly seaside course.
Bekele will try to emulate Kenyan Paul Tergat's achievement of winning the 4km and 12km titles five years in a row in Sunday's longer race. Tergat dominated both events from 1995.
Songok went one better than his bronze last year, finishing just a second behind Bekele, with Morocco's Adil Kaouch third in 10:57.
"No victories are ever easy but today was the toughest," Bekele told reporters after collecting his 17th world title in track, indoor and cross country.
"We've never finished this close. The course was very flat
Tirunesh Dibaba made it an Ethiopian double, producing a powerful finishing burst to defend her 8km title.
Dibaba, who won the 4km race last year, outsprinted Kenyan-born Lornah Kiplagat, who runs for the Netherlands, to win in 25:21.
"I knew I had better finishing speed so I wasn't too demoralised," said Dibaba, who missed nearly a week of training in the run-up to the championships through illness.
"I wasn't feeling very well. It was very hard but hopefully this will be the first of many gold medals."
Kiplagat finished five seconds behind Dibaba with Ethiopia's Meselech Melkamu third in 25:38.
The 4km races for both men and women will be dropped from next year's world cross country championships in Mombasa.