"Nikolaus Harnoncourt took his last breath peacefully surrounded by family," said the short announcement carried by the Austrian news agency APA.
In December Harnoncourt had announced his retirement, citing health reasons, in a farewell letter to the audience of the Wiener Musikverein, home to the Vienna Philharmonic orchestra.
"My physical capacities mean that I have to cancel all my upcoming projects," he wrote in an open letter to disappointed fans with tickets to a concert by the baroque ensemble he founded, the Concentus Musicus Wien, the weekend of his 86th birthday at the start of December.
"An era is over," the Musikverein's director Thomas Angyan told APA. "I didn't think so little time would pass between his retirement and his death. We must continue with the musical heritage which he left us."
Count Nikolaus de la Fontaine und d'Harnoncourt-Unverzagt was born in Berlin on December 6, 1929 to a granddaughter of a Habsburg Archduke and an Austrian count.
Growing up in Graz, southern Austria, he was already a contrarian thinker.
"Even when I was small, I always took the opposite point of view. I'm not someone who agrees," he said, suggesting that his rebellious intellect stemmed from being called up just two weeks before World War II ended.
Harnoncourt showed a keen interest in the arts early on, and studied the cello at Vienna's Academy of Music, joining the Vienna Symphony Orchestra as cellist in 1952.
But the authoritarianism of conductors enraged him.
"I used to ask them the 'why' behind their instructions. But the only reply I ever got was 'Because I say so'," Harnoncourt complains.
"Even the best musicians simply had to play. They were all part of an instrument called an 'orchestra', and the conductor was its player."
His intensive research into historical instruments and period performance practice led him to set up his own ensemble, Concentus Musicus, in 1953 and it began giving concerts in 1957.
Organised by the musicians themselves, with help from their wives and partners, they specialised in renaissance, baroque and early classical music by the likes of Bach, Beethoven or Haydn.
In 1969, Harnoncourt quit the Vienna Symphony and the decision -- and the ensuing financial and professional insecurity that entailed (he and his wife had had four children by then) -- was one of the best he ever took, he says.
In musically conservative Vienna, his insistent questioning raised hackles as it ran contrary to the norms of the established classical music scene.
But over the years, Harnoncourt's ideas have gained wider currency, and now even the world's greatest modern-instrument orchestras like the Vienna and Berlin Philharmonics use key elements of period practice, such as articulation, tempi, phrasing and the absence of vibrato.
In 1971, Harnoncourt made his debut as opera conductor at Vienna's Theater an der Wien, with Monteverdi's "Il ritorno d'Ulisse in patria". He went on to complete a now legendary Monteverdi cycle with director Jean-Pierre Ponelle at Zurich's opera house before embarking on an equally important and groundbreaking cycle of Mozart operas at the same theatre.
Not restricted exclusively to early music, Harnoncourt has recorded symphonic repertoire from classical to romantic and even 20th century music, including well-received discs of Dvorak and even Bartok.
In 2008, he conducted Stravinsky's opera "The Rake's Progress" at the Theater an der Wien to great critical acclaim and in the summer of 2009, he was to take on George Gershwin's "Porgy and Bess" at the Styriarte festival in his hometown of Graz.