Apparently, the delivery service MLBU uses did not show up in time for the game, according to Dan Hayes. The truck did arrive later, and they changed into MLB-approved pants between innings. (Just in time for Baker to eject the Twins manager.) And this isn't the first time this has happened (see here).
I'm about 99% sure the plate pants he was wearing were not smitties, based on the texture- maybe the old fechheimers? Still better than nothing.