Of the members of the abbey, the government allowed only Fr. Cantera to be present at the exhumation.
The government of Pedro Sanchez, secretary-general of the Spanish Socialist Worker's Party, had pledged to exhume Franco's body.
It is spending some $70,000 on the exhumation and re-burial, the BBC reported.
About 100 supporters of Franco protested the exhumation outside El Pardo cemetery Thursday.
Franco's grandson, Francisco Franco y Martinez-Bordiu, told Reuters that "I feel a great deal of rage because [the government] has used something as cowardly as digging up a corpse as propaganda, and political publicity to win a handful of votes before an election."
Spain is due to hold a general election Nov. 10.
Franco's family tried to block the exhumation in court, but lost its appeal. They also asked that if his body were re-interred, it be moved to Almudena Cathedral in Madrid, but this, too, was rejected.
Fr. Ramon Tejero said Mass at the Franco family mausolum in El Prado cemetery after the re-burial.
In January, Alessandro Gisotti, then-interim director of the Holy See press office, said that the exhumation of Franco is a "matter that concerns his family, the Spanish government, and the local Church."
Bishop Luis Javier Argüello Garcia, Auxiliary Bishop of Valladolid and secretary general of the Spanish bishops' conference, said on numerous occasions that the Church "is not opposed" to the exhumation of the remains of Franco according to the ruling of the Supreme Court, but asked that the country "look forward" and not "reopen wounds."
Numerous leftist groups have proposed demolishing the 150 meter high cross that presides over the Valley of the Fallen, to make it a "memorial." Some have also called for the site to be deconsecrated and the abbey closed.
(Story continues below)
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