The Chicago Board of Elections held off on printing the ballots until an Illinois appellate court ruled on the residency matter.
In a 2-1 opinion, the court ruled Monday that Emanuel's name can't be on the ballot because he didn't live in Chicago the year before the election.
"We're going to press with one less candidate for mayor," said Board Chairman Langdon Neal.
He conceded that the Illinois Supreme Court, should it take up the case, could allow Emanuel on the ballot, but said that time is of the essence.
"We can't wait and stop what we're doing to adjust to every possibility that may occur. We have an election to run and we're going to start with that election," he said.
Early voting begins next Monday, Jan. 31, but that process uses touch-screen ballots which can be more easily updated.
A spokesman said the paper ballots have already been proofed and could begin printing on Tuesday. Absentee ballots will be printed first, but an order for two million ballots without Emanuel's name has been placed, said Chicago Board of Elections spokesman Jim Allen.
Still, about 200 digital ballots have already been sent via email to residents overseas.
"The email works as a safeguard so that in the event someone doesn't receive the official mailed ballot, they can still print out that emailed ballot and send that in from overseas," said Neal.
The ballots were blank but accompanied by a list that did include Emanuel's name.