The party enjoyed a double success in Fife, winning the Dunfermline Central seat from the Conservatives and also taking one in Rosyth after increasing their vote share there by 16.5 percentage points.
Further north, a third new SNP councillor was elected to represent the Inverness Central area on Highland Council.
Derek Glen was selected to represent the Dunfermline Central ward, while former councillor Sharon Green-Wilson won back her seat in Rosyth after slumping to fourth place in 2017.
The wins push the SNP majority on Fife Council to six, with 30 councillors.
• READ MORE: Why this Brexit election is such good news for the SNPMeanwhile Emma Rodwick won in Inverness Central.
After the votes were counted there on Friday morning, SNP leader and First Minister Nicola Sturgeon tweeted: "What a result! That's 3 out of 3 SNP victories in yesterday's by-elections."
Drew Hendry, the SNP's candidate for Inverness, Nairn, Badenoch and Strathspey in next month's General Election, claimed the local authority results show voters are getting behind Ms Sturgeon's party.
Mr Hendry said: "This hat-trick of stunning election victories shows that voters are backing the SNP to beat the Tories, escape Brexit and put Scotland's future in Scotland's hands - not Boris Johnson's.
"The SNP has a clear, strong and positive message - and as the main challenger in every Tory-held seat in Scotland, only a vote for the SNP on December 12 can lock the Tories out of government and ensure the people of Scotland have a choice over our future.
"At the General Election on December 12, a vote for the SNP is a vote to stop the Tories, get away from the Brexit mess and protect Scotland's right to choose our own future - so we can build the fairer, more equal and prosperous country we all want to see."