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, 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.
MacDonald (17-2), who came into his fight as the No. 2 contender in the 170-division, controlled Woodley from the middle of the first round, using his superior reach to keep the two-time All-American wrestler at bay, while also connecting with both kicks and punches.
All three judges scored the fight 30-27 for the 24-year-old MacDonald.
MacDonald took Woodley down 2 minutes into the third and final round and relentlessly pounded the No. 3-ranked welterweight until the bell sounded.
MacDonald’s team rushed into the octagon to congratulate their fighter as the crowd roared in approval.
The soft-spoken MacDonald lost to Robbie Lawler in a split decision at UFC 167, but rebounded to take a unanimous decision against Demian Maia at UFC 170.
The 32-year-old Woodley (13-3), who scored a technical knockout of Carlos Condit at UFC 171, said before the fight he expected the crowd to be split, but the Canadian support found its way firmly behind MacDonald from the start.
Other winners on the card included former heavyweight champion Andrei Arlovski and light heavyweights Ryan Bader and Ovince Saint Preux.
Former NFL quarterback Tim Tebow attended the event and was booed by the crowd when he was shown on the big screens perched around Rogers Arena.
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