Babbitt told ABC News he expects pilots will embrace the program, and at least initially pilots groups have been supportive of the change.
"The Air Line Pilots Association supports a change in FAA policy on antidepressant medications," the group said in a statement. But "we are currently reviewing the FAA's new policy proposal and will comment accordingly."
"Our recommendation was six months [grounded observation]," said Aircraft Owners and Pilots Association spokesman Chris Dancy, "but we're comfortable with the 12 months because it does lay out a path that can get [pilots] back into flying."
Babbitt believes the new policy will also reassure the general public regarding safety.
"People that are in this program are going to be carefully monitored as they go forward," he said. "This is not just a one-stop -- you get this and go on and nobody pays attention."
Medical experts for the most part agree. Second-generation antidepressants, including the four drugs approved by the FAA, are widely believed not to pose risks of sedation or impair cognitive ability.
"I have not seen studies showing that the newer generation of antidepressants affect reaction time to the point where it would affect [a pilot's] flying abilities," said Dr. Murali Doraiswamy, chief of biological psychiatry at Duke University Medical Center.
"Most people that [have depression] are very debilitated by their condition… they describe it as a 'black fog,' an 'anchor' weighing them down," said Doraiswamy. And for many people, "from college professors to airplane pilots to machinery operators and CIA officers," antidepressants can improve quality of life and job performance.
There were more than 600,000 licensed pilots in the U.S. in 2008, according to the FAA. 124,000 fly commercial planes.
By law, pilots are annually required to answer questions about their health, including arrests and convictions for alcohol, and can face penalties for perjury, including revocation of their licenses.
Pilots are forbidden from using narcotics, medication for seizures, anxiety conditions and stimulants, according to an FAA spokeswoman. They're also barred flying after taking over-the-counter medication that might make them drowsy, such as Benadryl or NyQuil.
Under the new rules, depressed pilots consulting a therapist or psychologist instead of taking medication will remain barred from flying while in treatment.
Australian and Canadian aviation guidelines already allow some pilots to fly while taking antidepressant medication.
More than 10 percent of the U.S. population take antidepressants, according to a 2009 Columbia University study, making the drugs the most commonly prescribed class of medication in the country.