She is first player since Serena Williams in 2015 to pull off the feat. It propelled her to the top of the world rankings for the first time.
"Hey everyone," Osaka tweeted. "I will no longer be working together with Sascha. I thank him for his work and wish him all the best in the future."
Bajin, a former hitting partner to Serena Williams, responded: "Thank you Naomi. I wish you nothing but the best as well. What a ride that was. Thank you for letting me be part of this."
Osaka beat Petra Kvitova on 26 January in three sets to add the Australian Open to her US Open title from September 2018.
The Japanese star is the first Asian to hold top spot since the ranking system was computerized in November 1975.
Osaka linked up with Bajin in late 2017 when she was ranked 72nd in the world. During 2018 she won her first title on the senior circuit at Indian Wells before claiming her first Grand Slam title in New York.
Former Grand Slam champions Billie Jean King, Martina Navratilova and Chris Evert have all paid tribute to Osaka's rise.
"Winning back-to-back Grand Slam tournaments is a rare and special achievement and I'm thrilled these results have propelled Naomi to the top of the women's game," said Evert, the first WTA world number one.
"Her exciting brand of tennis, coupled with the dignity she displays on and off court, is a winning combination that tennis fans really embrace."