Colin Clark won in Inverurie and District with a gain from the Liberal Democrats, while Iain Taylor was elected in Banff and District in a gain from the SNP.
Both candidates campaigned strongly on opposition to SNP plans to raise council taxes for more than 40% of households in Aberdeenshire and spend the extra income in other parts of the country.
Leader Ruth Davidson said the result should serve as another signal – following the party’s success in May’s Holyrood election – that only Scottish Conservatives can beat the Nationalists.
Both Banff and Inverurie are represented at Holyrood and Westminster level by the SNP. The Scottish Conservative vote was up by 21.6% in Banff and 21.3% in Inverurie.
Ruth Davidson said: "This double win proves once again that the Scottish Conservatives are the party which can take on and beat the SNP, including in Alex Salmond's backyard.
"It's also vindication for our local campaign against the SNP's unfair council tax plans which would strip millions of pounds from the north-east.
"The message is clear: the SNP must start listening to the people of Scotland who want them to focus on the day job of governing - not obsess over a second referendum on independence."
Alexander Burnett, Scottish Conservative MSP for Aberdeenshire West, added: “The local campaigns were strongly focused on the council tax issue.
“More than 40% of households in this area will face an increase, with an estimated £8.6million additional burden on taxpayers at a time when the local economy is struggling.
“To make matters worse, that income will then be clawed back and spent in other parts of the country.
“People in Banff and Inverurie have sent a clear message to the SNP that it is time to give the North East a fairer deal. Our councils are among the lowest funded in the country and NHS Grampian is being short-changed to the tune of millions of pounds this year.
"Huge credit is due to our hard-working teams and great local candidates Colin Clark and Iain Taylor, who will be a strong voice on Aberdeenshire Council for their respective wards."