An official statement issued by the Archbishop's Council said the royal family had undergone its suffering with gentleness, patience and humility.
The Archbishops' Council, the Church's highest ruling body, also voted to canonise 853 other 20th Century martyrs, many of them priests and monks put to death during the Soviet era.
Nicholas II, his family, and four servants, were killed by a firing squad in the remote Siberian city of Yekaterinburg on 17 July, 1918, about eight months after the Bolshevik revolution.
An official statement issued by the Archbishop's Council said the royal family had undergone its suffering with gentleness, patience and humility.
The decision to canonise the Romanovs was taken by 144 of the Orthodox Church's most senior bishops, who gathered in the glittering chamber of council of Moscow's Christ the Saviour cathedral.
Seated beneath a gigantic mosaic of the 12 apostles, the bishops considered a list of more than 800 names being considered for sainthood.
But by far the most famous names on the list were those of the imperial family, whose bodies were burned, doused with acid and thrown into a pit.
They were exhumed in 1991, after the Soviet collapse.
After years of genetic tests and disputes about their authenticity, they were buried in 1998 in St Petersburg. The remains of two of the children were never found.
Saintly or weak?
At a ceremony to be held this weekend in Moscow, Tsar Nicholas II will become the fourth Russian monarch ever to be made a saint.
For many Orthodox believers, he already is one. Miracles are reported on the anniversary of his abdication and at the place where he and his family were killed.
But others in the Church have their doubts, accusing the tsar of being stubborn and weak, of clinging to power and of having a mistress.
In July, Russian Patriarch Alexei II stressed that any canonisation should take place because of the manner in which the tsar died, and not because of his actions.
Devotees of the former tsar have made fantastic claims about his powers - even after his death.
However, some Church leaders agree with the Soviet line - that the tsar and his family epitomised the excesses of the imperial era.
Canonising the family as so-called 'passion bearers' the lowest rank of sainthood, appeases supporters of Nicholas II, especially nationalists who want a return to the monarchy, without endorsing the way he ruled, Church officials said.
"It will be clearly explained that this is not about Nicholas being canonised as a monarch," said Father Hillarie Alfeyev, head of the Orthodox Church's external relations department.