i'd say it depends on wether minato can put a seal on him before madara activates his rinnegan, which is quite feasible. thing is shinobi with dojutsu usually only pull out their ms/ems when needed, like madara to block naruto's chou rasengan and rasenshuriken, sasuke to block jutsu etc. you don't come face to face with an opponent and power up ms right away, because of the chakra drain.
whereas minato is way more direct, throw kunai, engage in taijutsu in an attempt to mark with a teleporting seal, and nail them with rasengan. which gives him a good shot of winning imo.
but if madara manages to survive that, which i'm unsure about, then he has the overwhelming advantage. only thing for minato to do then would be to run around whittling down madara' chakra due to susanoo, because he's not getting through it.