The First Minister was urged by Scottish Conservative interim leader Jackson Carlaw to support Mr Johnson's plan if she was determined to avoid a no-deal Brexit, warning that it was the "eleventh hour" and compromise "on all sides" was needed to reach a negotiated settlement.
However, Ms Sturgeon said Mr Carlaw "had no credibility", after shifting his position "in a heartbeat" from being an "enthusiastic Remainser to a Boris Johnson loving no-deal Brexiteer".
In heated exchanges at Holyrood, she said the deal did not look as though it would be accepted by the EU, that it broke "all the promises made to Ireland at the start of the Brexit process" and added: "I won't support something like that, because Scotland doesn't support that. If Jackson Carlaw was interested in standing up for Scotland, as opposed to simply standing up for Boris Johnson, he wouldn't be supporting that either."
Raising the issue at First Minister's Questions, Mr Carlaw said the deal had "attracted support from people who want to leave with a deal" and that while the First Minister "says she'd do anything possible to stop a no-deal despite three opportunities this year, her MPs have never voted for a deal, does she regret it?"
Ms Sturgeon said: "My alternative to no-deal is no Brexit. That's what the people of Scotland voted for. All the efforts I made at compromise to keep us in the Single Market and Customs Union were spurned by Theresa May. Jackson Carlaw has brought the Scottish Tories into line with his Westminster bosses, but in doing so he has abandoned the interests of the Scottish people".
Mr Carlaw hit back and said: "The real shame is a First Minister who is prepared to conspire to make Jeremy Corbyn the Prime Minister of this county. The First Minister just confirms that there's not been a referendum this century whose result she's prepared to implement - that's not democracy.
'The SNP doesn't want a deal'
"The First Minister has said she wants a deal but now won't vote for one. If the First Minister had the courage of her convictions she would have voted for a General Election several weeks ago - she had her chance but once again her MPs were all talk and no action.
"The SNP doesn't want a deal, it's not prepared to respect or implement the result of the referendum."
Ms Sturgeon said Mr Carlaw had made a "miscalculation" that backing Boris Johnson was the best way to remain leader of the Scottish Tory party, and while he urged continued "intensive discussions" between the EU and the UK governments, she said it was more a case of "intensive care" for Boris Johnson's proposals.
"I don't see any indication they will be acceptable to the European Union," she said. "I want Scotland to remain in the European Union."