The machine recount showed Gov. Scott, a Republican, with a lead of 12,600 votes or 0.15 percent over Democratic incumbent Nelson, triggering a manual recount under state law.
Both the Senate race and the race for the state's agricultural commissioner will be sent to a hand review of overvotes and undervotes -- ballots where a voter marked more or fewer candidates than allowed.
Earlier Thursday a judge ruled that thousands of provisional and mail-in ballots in Florida that were initially set aside now have more time to join the recount.
Voters who cast the provisional or mail-in ballots, but were rejected because of mismatched signatures, now have until Saturday to verify their ballot, Judge Mark Walker of the U.S. District Court in Tallahassee ruled.
"This should give sufficient time, within the state's and counties' current administrative constraints, for Florida's voters to ensure their votes will be counted," Walker wrote in his decision.
The decision affects about 4,000 ballots in 45 counties and an unknown number in the other 22.
"Let this court be clear: it is NOT ordering county canvassing boards to count every mismatched vote, sight unseen," the ruling states. "Rather, the county supervisors of elections are directed to allow those voters who should have had an opportunity to cure their ballots in the first place to cure their vote-by-mail and provisional ballots now."
In his ruling, Walker said the state's process for verifying mismatched signatures had been applied incorrectly, making it difficult for voters to make changes before the original Nov. 5 deadline.
The state had argued extending any deadline to Saturday would erode faith in the election, but Walker disagreed.
"Any potential hardship imposed by providing an actual opportunity to challenge the determination that a signature does not match, and thus, a vote does not count, is outweighed by the risk of unconstitutionally depriving eligible voters of their right to vote and have that vote counted," Walker wrote.
The ruling could be a deciding factor for the Senate race between Scott and Nelson.
Scott's campaign is expected to appeal the decision.
This issue is separate from the machine recount being done in Broward and Palm Beach counties. Broward officials said they would finish their recount by the 3 p.m. Thursday deadline.
Palm Beach County missed its 3 p.m. deadline to complete the mechanical recount after its ballot-counting machines overheated and a federal judge in Tallahassee rejected a motion to extend the deadline.
Palm Beach election officials worked in a giant warehouse with no windows, one bathroom and a vending machine during the recount.
"We are doing the best we can," Susan Bucher, elections supervisor, told the Palm Beach Post.