Running under ideal weather conditions the 10,000m world champion improved Kenya's Rhonex Kipruto's previous World record of 13min 18sec set last month in Valencia by 27 seconds.
Cheptegei won the 10,000m gold at the world championships in Doha last October, while Kipruto took bronze.
“Wow, this is a really great," said Cheptegei.
"I had sub 13 minutes in my mind today so when my legs felt good during the race I decided to really go for it. To take this many seconds off the record makes me very happy and is a great first test for me in an important season.”
Cheptegei's personal best in the 5000m in the stadium stands at 12:57.41.
Jimmy Gressier of France took second place in 13:18, to break the European record of 13:29 set by Julien Wanders in this race last year.
Cheptegei also improved the fastest 5km time ever of 13:00 set by Kenya's Sammy Kipketer 13:00 clocking in Carlsbad, USA, in 2000, well before the 5km became an official world record event in November 2017.