Sir John, a world expert on the music of J S Bach, took the top honours at the Classic FM Gramophone Awards in London yesterday, one of the most prestigious dates in the classical music calendar.
He took the decision to release the music himself after the label Deutsche Grammophon pulled the plug on him in 2000 after nearly 20 years, just as he was about to embark on a tour of Europe performing all of Bach's 200 cantatas.
The label's decision was a serious blow to the project's budgets. But Sir John went ahead anyway and then set up his own record label to release the results.
James Jolly, editor of Gramophone magazine, said: "Sir John Eliot's Bach Cantata Pilgrimage in the millennial year 2000 remains one of the most ambitious and uplifting musical undertakings ever."
Sir John said there was no feeling of triumphalism. "But it's awfully nice that a project that cost huge effort and put one through the mill - in terms of the anxiety and in terms of the stamina needed for 89 concerts in 13 countries in one year - has been recognised."
Placido Domingo, who this year released a recording of Wagner's Tristan und Isolde won the Classic FM's listener's choice. "He really is the complete modern musician," Mr Jolly said.
The label of the year award went to the bargain-priced record company Naxos, which was praised for its "visionary zeal".
The Lindsays, the Sheffield-based string quartet who retired this year after 40 years, were given a special achievement award, while the artist of the year award was won by Michael Tilson Thomas, music director of the San Francisco Symphony. Marilyn Horne the great American mezzo-soprano, won the lifetime's achievement award, which was presented to her in New York last week.