Independent John Cowe won at Heldon and Laich at the fifth stage of a daytime count under what was effectively the alternative vote system.
The result is the fifth council contest in Scotland since the referendum deal and all have shown a drop for the SNP – averaging 7.9 per cent. It lost seats in three of the by-elections.
An SNP spokesman said: “While the SNP secured a seat in this multi-member ward in 2012, coming second place on the single transferable vote method, the by-election was for one seat only on the alternative vote system when we again achieved a strong second place. Therefore, the results are not comparable.”