The unofficial count stands at 25,090 for Amodeo, a three-term incumbent and a union crane operator, and 25,088 for Mazzeo, owner of a fruit and vegetable store and the mayor of Northfield.
The board spent about 20 hours examining provisional ballots over two days this week.
The ruling was perceived as a victory for Mazzeo, who said he was "ecstatic" and praised the process as fair.
Amodeo said, "Let's go count the ballots and see where we stand."
The ballots yet to be opened are all challenged by Republicans and include 32 from Atlantic City and 56 from Pleasantville, both with mostly Democratic voters - though Atlantic City voted for its first Republican mayor in more than two decades.
The provisional ballots already opened decreased Amodeo's original lead of 274 to just two.
Democratic lawyer Chris Orlando argued that an assisting poll worker's signature without the required certification of disability, or as merely an indication of having instructed the voter on the provisional ballot process, was at worst a mistake on the poll worker's part and should not penalize the voter.
Republican lawyer W. Timothy Howes argued that the aid was improper and that counting those ballots would undermine the election's integrity.
Mendez called the lack of disability certificates a "technical deficiency" and said the poll worker's indication of aid could have meant that the worker was offering instructions about the provisional ballot, which poll workers are required to do.
"To rule these provisional ballots should not be counted in light of these deficiencies - and I acknowledge they were deficiencies - would be to preclude those votes from being counted," Mendez said.
He said his ruling did not mean that the ultimate result could not be challenged or contested.
He cited case law that votes should not be set aside where there is no indication of fraud or undue influence and said regulations should be "liberally construed" so as not to unfairly disenfranchise voters.
He essentially acted as the tiebreaker on ballot challenges where the Board of Elections had voted 2-2.
He accepted all but one ballot, where the challenge was that the signature on the ballot did not match the registration. The ballot and the original signatures were projected on a screen so the courtroom, packed with partisans, could see for themselves.
There were 10 with signature issues, two of which also had a poll-worker assistance issue.
Provisional ballots are issued at the polling place when the voter is either not in the book as being registered or had been issued a mail-in ballot. The ballots must be verified by the Board of Elections to determine that the person was registered and that no mail-in vote was received.
Democrats had come prepared to call poll workers to the stand to testify that their signatures only indicated that they helped with the process, not with the voting itself.
"They sit off to themselves," one such poll worker, Fran Peskoe of Margate, said, referring to voters she had helped.
But the judge said that kind of evidence would be heard only if there was a subsequent contest of the election results, which must be certified Tuesday.