A lack of guarantees from the UK Government over how the airport’s expansion would benefit Scotland was blamed for the party’s decision.
It has led to opposition politicians claiming the SNP’s eco-friendly image is in “tatters” and that they have “lost all credibility”.
Scottish Greens co-convener Patrick Harvie said: “We know the SNP at Holyrood have previously done the aviation lobbyists’ bidding, in trying to hand out tax cuts to the industry.
“Now the SNP MPs are sitting on their hands when anyone motivated by the environment or social justice would be voting to oppose Heathrow expansion.
“SNP ministers’ regular claims to be climate change leaders are now in tatters.”
Scottish Conservative shadow finance secretary Murdo Fraser added: “The third runway project stands to secure as many as 16,000 jobs in Scotland thanks to the work that will be required across the UK.
“The SNP knew that - which is why it originally backed Heathrow’s bid.
“They could have acted in the Scottish interest and in the interests of passengers and workers across Scotland.
“Instead, they have done Nicola Sturgeon’s bidding and put her interests before the country’s.
“It is an appalling decision. Every day, the SNP scaremongers about the damage that Brexit may do to the economy.
“Yet here it is attempting to wreck a major piece of infrastructure which would massively boost Scotland’s economy. The SNP has lost all credibility.”
The Scottish Government has previously given its backing for plans to build a third runway at the airport.
However, the SNP’s transport spokesman Alan Brown said he would abstain from the vote on Monday.
He told the Commons: “I’ve been supportive to date and I certainly won’t back against these proposals because what I hope the opportunities are for Scotland, but given the fact the UK Government cannot and will not provide these guarantees I also cannot unfortunately vote with the Government.”
Mr Brown said he wanted guarantees for the number of domestic flight slots at Heathrow.
This led Transport Secretary Chris Grayling to intervene to say the airport had agreed with the SNP and the Scottish Government that it is prepared to set aside 200 slots for connections to Scotland.
MPs are to decide on Monday evening whether to approve the expansion of Europe’s busiest airport, with more than 40 Labour members saying they would go against party policy and support the Government’s decision.