Johnson put on a display of speed against the challenger, who scored a couple of takedowns but was never really a threat. The fight was scored 50-45 by all three judges.
In the co-main event, Canadian welterweight Rory MacDonald beat Tyron Woodley in an impressive unanimous decision in the most exciting bout of the night.
MacDonald was mentored by Georges St-Pierre before the former champion stepped away from the sport late last year.
Johnson almost connected with a spinning kick with under a minute to go in the fifth and final round, but Bagautinov was able to avoid the blow to send the bout to the scorecards.
The 5-foot-3 Johnson (20-2-1) won the UFC's inaugural flyweight title in 2012 and has now successfully defended the 125-pound belt four times.
The 27-year-old who fights out of Parkland, Washington, and graduated from Washington High School, had expected the 5-foot-4 Bagautinov (13-3) to pose a unique challenge because the 29-year-old Russian specializes in Sambo fighting, a form of mixed martial arts that he has never faced.
However, Baugatinov was overmatched and at times just seemed happy to be in the ring with Johnson, even hugging his opponent before the start of the fifth round.