Very Simple. In the confrontation, Minato analyzed Madara's Gududama, and came up with a hypothesis. The conclusion was that the Gududama must be in a certain range for Madara to be able to control them - this was around 70+ meters. So, Minato knew that once he takes the Gududama far from Madara, they become fodder and they cannot explode or do anything to him.
Conclusion: Minato teleported them to another place - probably Konaha - where he can get rid off them.