Charges were laid against Essendon, James Hird, Mark Thompson, Danny Corcoran and Dr Bruce Reid on Tuesday night for bringing the game into disrepute.
The AFL said in a press conference no infraction notices would be issued under the anti-doping code "at the present time".
It emphasised this could change if new information came to light as the investigation continued.
However, for the time being, Watson's medal victory will stand.
"At the current time, you'd have to say no, [Watson's medal is not up in the air]," former AFL football operations manager Adrian Anderson told 3AW on Wednesday.
"On all the evidence to date, it's been made clear that the AFL's view is there's insufficient evidence to charge individual players with individual offences under the anti-doping code."
On Tuesday night, Watson said the players felt 'vindicated' by the ruling that no individual player had violated the anti-doping code.
"As we've said all along, none of us believed we'd done anything wrong in relation to the 2012 supplements program," he said.
"We’ve fully co-operated with every part of the ASADA investigation and we've always said we've got nothing to hide.
"We feel vindicated by this announcement and hope this helps confirm the faith of our supporters and the broader football public that, as professional sportsmen, we would never do anything to compromise the integrity of the game, our team, or our own values."
Watson statement in full
Charges have been laid ahead of a hearing at AFL House on August 26 despite the ASADA report on which they were based being unfinished.
Anderson said the fact the report wasn't completed didn't matter when it came to the AFL laying the charges.
However, he did say there were questions over the timing of the decision.
AFL statement in full
"I think they're very separate, so the AFL has made a call here that it's got sufficient information at the moment to justify a charge of conduct unbecoming," he said.
"I don't think it's really to the point as to whether the ASADA enquiry is finished or not as to whether they have sufficient information.
"We don't know what that information is, it hasn't been disclosed at the moment - hopefully it will at some point in time so we all understand.
"To say there's an interim report, it doesn't preclude the AFL from issuing a separate charge for conduct unbecoming under its rules, but certainly there are legitimate questions about whether it's the right timing or not."
No issue with charges: WADA
Anderson said a question that also needed to be answered was why sacked biochemist Stephen Dank had not been approached by ASADA for an interview.
He also said while he had no reason to believe the investigation hadn't been handled well, there was a "real lack of transparency and understanding" when it came to ASADA and its position from earlier in the year to now.
Veteran Bomber Dustin Fletcher said it was a relief the players had been cleared of infraction notices at this stage.
"It's still on-going, disappointing Hirdy and Reidy and the boys have been charged, but that's how it is and we'll move on," the 38-year-old said on Wednesday.
"We know a few things a lot of people don't. We were always pretty confident."
Twitter: @AFL_JenPhelan
"I think they're very separate, so the AFL has made a call here that it's got sufficient information at the moment to justify a charge of conduct unbecoming," he said.
"I don't think it's really to the point as to whether the ASADA enquiry is finished or not as to whether they have sufficient information.
"We don't know what that information is, it hasn't been disclosed at the moment - hopefully it will at some point in time so we all understand.
"To say there's an interim report, it doesn't preclude the AFL from issuing a separate charge for conduct unbecoming under its rules, but certainly there are legitimate questions about whether it's the right timing or not."
No issue with charges: WADA
Anderson said a question that also needed to be answered was why sacked biochemist Stephen Dank had not been approached by ASADA for an interview.
He also said while he had no reason to believe the investigation hadn't been handled well, there was a "real lack of transparency and understanding" when it came to ASADA and its position from earlier in the year to now.
Veteran Bomber Dustin Fletcher said it was a relief the players had been cleared of infraction notices at this stage.
"It's still on-going, disappointing Hirdy and Reidy and the boys have been charged, but that's how it is and we'll move on," the 38-year-old said on Wednesday.
"We know a few things a lot of people don't. We were always pretty confident."
Twitter: @AFL_JenPhelan
