User blog comment:FairyRaven/Fairy Tail Chapter 346: Retrogression Magic, Review and Commentary/@comment-7418318-20130802133028/@comment-7418318-20130802154112

That was explained in the story itself. With his Sharingan Sasuke can see Naruto's chakra-flow and adapt his own to match it.

And I too have problems telling them apart and it doesn't even make any sense in the first place. Naruto looks like that due to the Kyuubi chakra. Since he's not a Jinjuuriki there's no reason for Minato to look like that other than a forced and stupid "Oh look! Like Father, like son!" moment.