The SPÖ has ruled out a coalition partnership with the FPÖ - and will be discussing whether to continue in partnership with the Greens, or form a coalition with the ÖVP, which saw its score fall 5.3 points to 8.7 percent, below 10 percent for the first time.
The ÖVP (known as the 'Black' party) was in fourth place behind the Greens on 11.1 percent. The head of Vienna's Greens, Maria Vassilakou, has said she will not step down despite the party scoring 1.99 percentage points less than in 2010.
The final results may not be known until Tuesday as 160,000 postal votes are still being counted.
Fifteen years after the FPÖ stunned Europe by entering the federal government under the late Jörg Haider, the populist party won 31 percent of the vote in the city state, preliminary results showed.
Under Heinz-Christian Strache's leadership the party gained 5.3 percentage points compared to the last election in Vienna in 2010, when their score soared 11 percentage points.
In Upper Austrian state elections last month the FPÖ gained 15.1 percentage points, and in Styrian state elections earlier this year 16.1 percent. A major issue for voters has been the arrival of hundreds of thousands of refugees and a rise in the number of asylum claims.
The SPÖ, which has ruled ‘Red Vienna' uninterrupted since 1945, scored 39.4 percent, down 4.9 points, adding to a similar drop in support in 2010.
The election results look set to change the city's political landscape. Excluding postal votes, the FPÖ came first in municipal elections in two Vienna districts for the first time - Floridsdorf and Simmering.