A total of 19 SNP councillors were elected, up from 16 in 2012, as the Conservatives surged to 11 from three and Labour's total halved to nine.
Labour's finance convener Willie Young was among the casualties, but party group leader Jenny Laing kept her seat on the council.
In Aberdeenshire, the Conservatives overtook the SNP. In Moray, the SNP was the biggest party.
Mr Young said after the Aberdeen result: "The Conservatives have done very well. You've got to accept you can lose. That's politics for you."
By BBC Scotland political editor Brian Taylor
Let's talk numbers - there have been boundary changes which mean that some comparisons are made with "notional" outcomes in 2012, the last time these councils were contested.
On that count, the SNP are notionally down by a fractional seven seats. However, in terms of absolute numbers, the Nationalists have ended up with more councillors than in 2012.
Plus the SNP are the largest party in Scotland's four largest cities - including Glasgow, where jubilant supporters attended their ousting of Labour. They have waited decades for that.
Read more from Brian
In Aberdeenshire, the Conservatives had 23 seats, up from 14, while the SNP fell eight to 21. The Lib Dems gained two to 14, independents fell from 12 to 10, and labour dropped from two to one.
In Moray, nine SNP councillors were elected (down one) - along with eight Conservatives (up five), eight independent (down two) and one Labour (down two).
Orkney elected its first ever Scottish Greens councillor, while the SNP gained its first representative in Shetland.
Steve Sankey was elected in the East Mainland, South Ronaldsay and Burray ward of Orkney Islands Council.
Robbie McGregor won the uncontested Shetland South seat for the SNP.
Shetland's political leader Gary Robinson lost his Shetland West seat.
The SNP has become the biggest party on Aberdeen City Council.