The commotion began last week when Scalia flicked his fingers under his chin in response to a Herald reporter's question about people who question Scalia's impartiality because of his religious beliefs.
The newspaper termed Scalia's response a "Sicilian salute."
This week, Colbert, star of Comedy Central's "The Colbert Report," made fun of the newspaper and the jurist.
"There's an old saying where I come from. I honor you with all the treasure in my coin purse," said Colbert while grabbing his groin. "That's for you, Boston Herald!"
While the newspaper characterized Scalia's gesture as obscene, the jurist denied the claim.
"(Scalia) was just saying he had no opinion about the question the reporter was asking him," said Colbert. "I can sympathize because I've had my gestures misinterpreted dozens of times."