At a rowdy and often angered FMQ meeting, Scotland’s Tory leader said the First Minister had also “abandoned rural Scotland” by keeping the joint government agreement.
It was intended to cause a split between the two parties ahead of Saturday’s SNP Independence Party Conference in Dundee, which will also discuss the general election.
Some SNP MPs are unhappy at the prospect of campaigning to defend the Greens’ controversial policies.
Mr Ross also brought up former SNP Farm Secretary Fergus Ewing, who voted against his own government in a vote of confidence in Green Secretary Lorna Slater on Tuesday.
The SNP is now considering removing the party leadership from the Inverness-based MSP after he sided with the Tories in a call to sack Ms Slater for alleged incompetence.
Mr Ewing is a harsh critic of Ms Slater’s sponsored drinks container recycling scheme, which has been delayed until at least 2025 following a UK government decision.
Circularity Scotland, the company set up to run the scheme, went bankrupt this week, losing up to 60 jobs after the drinks industry refused to continue funding the scheme.
Also the state-owned Scottish National Investment Bank said it could lose £9million in public funds it had given Circularity Scotland to help cover its start-up costs.
At FMQs, Mr Ross asked Mr Yousaf if he planned to “fire Fergus Ewing”.
Mr Yousaf declined to reply, insisting it was a matter for the SNP group in Holyrood.
Mr Ross said: “This is a Government matter as it was a Government vote of no confidence in a Government Minister.” Certainly Humza Yousaf can be honest with people across Scotland if he takes it seriously that one of his own MSPs refused to support him?”
He said Mr Ewing had expressed a lack of confidence in Ms Slater “due to her terrible performance in office”, particularly her handling of the deposit return system.
Mr Ross said Mr Yousaf was willing to “lose a party stalwart who is committed to the Scottish economy” while keeping “an incompetent Green Minister” in government.
He also compared the situation to Mr Yousaf’s repeated refusal to suspend Nicola Sturgeon after she was arrested as a suspect and released without charge earlier this month.
The former First Minister was questioned for nearly seven hours by investigators looking into whether the £660,000 raised by the SNP for Indyref2 was spent on other things.
“It looks like Humza Yousaf, the First Minister who is not going to suspend Nicola Sturgeon, who is under police investigation, will suspend Fergus Ewing for challenging the Greens’ incompetence,” Ross said.
Mr Yousaf pointed out that the MSPs had rejected the motion of censure against Ms Slater.
He also said that the blame for delaying the deposit return scheme “clearly” rests with the UK Government, which said it must not include glass recycling.
He said: “The reason this Parliament backed the Government, Lorna Slater, when it came to this vote of no confidence is because they know it was the UK Government’s eleventh hour intervention that completely torpedoed the deposit return scheme .”
The exchange came ahead of the public announcement that Mr Ewing’s mother, SNP icon Winnie Ewing, had died aged 93.
The two leaders also clashed over rural issues at the opening of the Royal Highland Show in Edinburgh. Mr Yousaf quoted Martin Kennedy, President of the National Farmers Union Scotland, who had previously criticized Brexit.
Mr Ross then quoted Mr Kennedy speaking about the Scottish Greens this morning.
Mr Kennedy had said that “the intensification of the green agenda…is a matter of serious concern not just for rural businesses but for the Scottish economy as a whole”.
Didn’t that show the SNP had “abandoned rural Scotland,” Mr Ross asked.
“It is clearer than ever that the extremist Green Tail is wagging the SNP dog.
“Humza Yousaf has described the SNP Green Deal as ‘golden’, but Green influence is damaging to all policy areas.
“The extremist Greens in government appear to be driving much of the decisions of this SNP government. Their influence is detrimental to all policy areas.
“With the deposit return system, they are risking jobs and businesses.
“By farming, they are endangering their livelihoods in the countryside.
“In gender reform, they endanger women’s rights.
“When you fish, you are risking the future of the industry.
“In the case of oil and gas, they threaten Scotland’s energy security.
“The SNP has so little contact with mainstream Scotland because they are being dragged in that direction by the Scottish Greens.
“Why is Humza Yousaf, to use the words of one of his MPs, dancing to the tune of an extremist party?”
The First Minister said it was Mr Ross who was out of touch with the public as the leader of the “third party in Scotland”.
He said: “We are in this agreement because I think people want different political parties – yes, the SNP and the Greens have differences – to come together to work in the national interest.”
“But why else is this cooperation agreement so important? Because the biggest problem facing not just Scotland but the planet as a whole is the climate emergency, which threatens the sustainability of our planet.
“Where are the Conservatives when we keep coming up with measures to address the climate emergency? They are against every single measure.
“Why do they reject every single measure? Because frankly, they are turning into climate change deniers.”