Yes, Japan still uses physical time cards, and it doesn't look like they're going away anytime soon. I actually like them. For the bit of analog touch, for the ritual of starting and ending a day.

I had to go out to a conbini today to grab an onigiri for lunch. And passing the machine, I absentmindedly pushed my card into it. For some reason, the act was greatly amusing to my coworkers. "Going home already?" one of them asked, barely containing her laughter.

Fortunately, it turned out not to be a big deal. I was told to just punch it again in the evening.