It urged MPs to take its position into account in the critical Commons vote next week.
The industry body published a Brexit briefing, stating: “On balance, the draft Withdrawal Agreement and accompanying Political Declaration on the Future UK-EU Relationship stand up well against the Scotch Whisky industry’s Brexit priorities.
“The SWA therefore supports approval of the two negotiated texts by the UK and European Parliaments.
“If the deal is rejected, this will create considerable uncertainty for the industry and greatly increase the potential of a no-deal Brexit in March 2019.”
The announcement follows leading Scottish businessman Sir Ian Wood saying Theresa May’s deal is “workable” and better than the current situation with Europe.
He also warned against the risks of a no deal Brexit.
Scottish Conservative finance spokesman Murdo Fraser said: “This is another major player in the Scottish economy backing Theresa May’s Brexit deal.
“We now have senior representatives from Scotland’s most important industries - whisky, oil, farming and fishing, among others - saying this now has to happen.
“MPs voting on this now need to consider what’s important here, and who is worth listening to.
“And as for the SNP and Labour, if they troop through the lobby in attempt to force a no-deal scenario, the people of Scotland will simply not forgive them.”
He added the deal “honours the vote of 2016” and allows the UK to leave the EU without the “chaos and misery” likely in a no deal Brexit.