Speculation grew on social media this week after Breaking Defense magazine reported Nelson was a possible candidate due to his "strong relationship" with the president.
"Scott has toed the line between imprudent campaign-trail rhetoric and problematic state action," said U.S. District Court Judge Mark Walker in his ruling. "But he has not crossed the line."
After a statewide machine recount on Thursday showed the vote margin between the two candidates was less than 0.25 percent, Florida Secretary of State Ken Detzner officially ordered Florida's 67 counties to begin a manual recount of overvotes and undervotes.
The ruling came just hours before the 3 p.m. deadline for the statewide recount to be finished.
State law requires an automatic machine recount if a vote margin is less than 0.50 percent in a statewide race.
Florida is once again at the center of an election storm as candidates file lawsuits and allege voter fraud while their races head for likely recounts.
Florida Governor Rick Scott accused "unethical liberals" of trying to steal the Senate and governor races.
"When I won the presidency, at least my side felt pretty good," Obama said during a Miami rally on Friday.
The Democrats' slight leads come as President Donald Trump and independent Senator Bernie Sanders of Vermont make trips to the Sunshine State to stump for their candidates.
Scott, who's currently running a tight race to unseat Democratic Senator Bill Nelson, has long argued that he does not support efforts to rid the requirement for insurance companies to cover pre-existing conditions under the Affordable Care Act.
Parents of Parkland school shooting victims are rallying behind Senator Bill Nelson as he seeks re-election.
"Either Bill Nelson knows of crucial information the federal government is withholding from Florida election officials, or he is simply making things up," Florida Governor Rick Scott said Friday.
Offering few details as to what he was referring to, Bill Nelson's claim of Russian interference has left some local and state agencies both concerned and confused.
The president faced criticism from both sides for his pick to serve as senior space science adviser, lead the agency and manage its resources.