The pizzas were in response to a segment Stewart did on Wednesday about Chicago losing the claim of being home to the world's tallest building in the world to New York. In that segment Stewart said Chicago-style pizza is really more like a casserole.
"I don't know whether to eat it or throw a coin in and make a wish," Stewart said.
The anchovies on Emanuel's pizza may not have been an accident. There's a famous story that Emanuel, when he was working at the Democratic Congressional Campaign Committee, sent a rival a dead fish in a box, an homage to a famous scene in The Godfather.
In response to Emanuel's gift, Stewart's camp posted a Vine video of a dog sniffing a pizza and running away, according to DNA Info Chicago.
A spokesman for Emanuel's office told TPM on Friday they did not plan to respond to the Vine.
Watch the original Daily Show segment that started it all below:
This story was updated.