Worku finished in 2hr 09min 10sec, followed by Japan's Satoru Sasaki who clocked 2:09:47, and Kipruto with 2:09:54.
"The (road and weather) condition was good. At 30 kilometres, I was confident. So I pushed, pushed and... go," said Worku.
"I am very happy," he said.
The three men closely contested the lead in the final phase of the race, with the Africans running shoulder-to-shoulder and Sasaki a step behind them.
With four kilometres to go, Worku staged a duel with Kipruto, leaving behind Sasaki who still kept them in sight.
In the final three kilometres, the Ethiopian shifted into a higher gear and began a solo journey to the finish line.
Sasaki also caught Kipruto up on the track of the Ojiyama Athletic Stadium to grab second place.
Results from the Lake Biwa marathon on Sunday:
1. Bazu Worku (ETH) 2hr 9min 10sec
2. Satoru Sasaki (JPN) 2:9:47
3. Vincent Kipruto (KEN) 2:9:54
4. Yuki Kawauchi (JPN) 2:10:38
5. Ryosuke Fukuyama (JPN) 2:11:18
6. Rui Yonezawa (JPN) 2:11:59
7. Noriaki Takahashi (JPN) 2:12:04
8. Muryou Takase (JPN) 2.12:31