The 25-year-old shaved 10 seconds off the previous world record, set by Ethiopia's Yomif Kejelcha in Valencia in 2024, reclaiming a title he last held in 2021 when he clocked 57:31 on the same Lisbon course.
Kiplimo came close to an all-time best in Barcelona last year with a 56:42 run. However, that performance was not ratified by World Athletics due to illegal pacing assistance.
Kenya's Nicholas Kipkorir finished a distant second in 58:08, with compatriot Gilbert Kiprotich securing third place in 58:59.
"I'm so happy to break the world record," Kiplimo said. "After the first 10km, I thought the world record was possible. I tried to keep pushing the pace in the final two kilometres."