Mine had her's last month. She yelped when the vet did it, then a couple of times over the next few days, yelped when we picked her up in a certain way. We think her lymph nodes (under her front legs) were swollen - this happened within hours. She wasn't her usual self for 24 hours or so - very subdued but she did eat.
Might be that. Does he have a favourite treat? Maybe you could try tempting him with that? He'll be fine tomorrow. Mine seemed to take about a day to get over it. I've never had a dog have a reaction to it in the past so it was a bit scary for mine to be yelping and down for a day, but she's fine now.