Putin arrived in a car carrying a bouquet of flowers and accompanied, local media said, by a troupe of Cossack singers booked to serenade the newlyweds. He was on a stopover on his way to meet German Chancellor Angela Merkel outside Berlin.
Photographs showed Kneissl, 53, smiling in a long white and cream "dirndl" dress and talking to Putin as they danced in a vineyard in southern Styria province, the venue of her wedding to entrepreneur Wolfgang Meilinger. Putin - who made a toast in German at the wedding, according to the Kremlin - was pictured listening to her intently.
The invitation surprised many in Vienna and Moscow, particularly at a time when the European Union is at odds with Russia over its annexation of the Crimea region from Ukraine, and other issues.
There have been no reports that Kneissl - a polyglot Middle East expert without political affiliation - has a particularly close friendship with Putin. But she was appointed to her job by the far-right Freedom Party (FPO) which has a cooperation agreement with Putin's United Russia party.
FPO leader and Vice Chancellor Heinz-Christian Strache has expressed support for Russia and called for sanctions against Moscow to be lifted.
"SYMBOLIC AND HARMFUL"
Chancellor Sebastian Kurz and his conservatives, who control Austria's EU policy, have said Austria will toe the EU line - though they have also pointed to Austria's history of neutrality and its relatively warm relations with Russia. Kurz also attended the wedding.
Strache, who joined Austria's governing coalition last year, praised Kneissl on Saturday as a "bridge builder" as he congratulated the married couple and wished them "all the luck in the world and eternal love!"
The international coverage of Putin's visit would bring priceless publicity, he added. "A better advertisement for Austria, its wonderful nature, dreamlike landscape and real life hospitality cannot exist!"
"All the more symbolic and harmful to court the Russian president in this manner," he said.
Kremlin spokesman Dmitry Peskov told Russian news agencies that Moscow rejected the criticism regarding Putin's presence at the wedding.
Putin travelled to Germany later on Saturday to meet Chancellor Angela Merkel for talks about Syria, Ukraine, and energy matters.
Austria did not follow other members of the EU earlier this year in expelling Russian diplomats after Britain accused the Kremlin of involvement in the poisoning of a former Russian spy and his daughter in England - a charge Moscow denies.
Putin visited Austria in June on his first trip to the West after being re-elected as president.