Among those present in the city's main cathedral were Prince Albert of Monaco and Spain's former Queen Sofia, while small groups of well-wishers braved the rain outside holding up placards with slogans such as "Safe Journey, Prince".
A message of condolence from Pope Francis was also read out but the service attracted only limited interest in Italy, reflecting the fact that Vittorio Emanuele lived much of his life in exile in Switzerland.
His 51-year-old son, Emanuele Filiberto, bent down and kissed the coffin as it was placed into a hearse. He was flanked by his mother, Marina Doria, the widow of Vittorio Emanuele.
Born in the southern Italian city of Naples, Vittorio Emanuele left his homeland as a child when his father Umberto II was forced to depart following the 1946 national referendum that abolished the monarchy and established a republic.
Vittorio Emanuele had declared himself King of Italy and long battled the rule in the Italian Constitution which barred all male members of his family from returning to the country.
He did finally return to Italian soil in 2002, after parliament lifted the ban, travelling to Rome for a brief visit and an audience with Pope John Paul.
But he met a cool reception on his return, the House of Savoy's image having been sullied by its World War Two-era association with fascist dictator Benito Mussolini and Vittorio Emanuele's own legal problems.
(Reporting by Massimo Pinca in Turin; Writing by Keith Weir)