Molina, who died at the age of 91, never wavered in his loyalty to the dictator who ruled from 1939 until 1975.
Numerous mourners at Molina's funeral in the resort town of Nerja in southern Spain, where the ex-minister lived, raised their arms as the coffin passed, while some sang the "Cara al sol" anthem of the Spanish Phalanx fascist party, an AFP photographer said.
Molina's son Luis Felipe had announced the death of his father in a letter of mourning on the Francisco Franco National Foundation website.
"They may take your name off the walls of the street," he said, referring to ongoing moves by towns to remove street names honouring Franco era figures.
"But nothing will take away the gratitude of thousands of families."
Molina's son-in-law Alberto Ruiz Gallardon, a former conservative mayor of Madrid and ex-justice minister, was among the pallbearers.
The letter added that for his funeral, "today we have dressed you again in your blue shirt," the clothing of the Spanish Phalanx party set up in 1933.
In the last two years of the Franco dictatorship, Molina served as housing minister, then as deputy head of the Nationalist Movement -- the fascists' vehicle for social, corporate and economic policy -- and finally deputy head of government.
In 2014, an Argentine judge tried to have Molina and other senior Franco officials extradited for human rights abuses.
Spain rejected the bid, as it had passed an amnesty law in 1977, two years after Franco's death, for crimes committed under his regime.
An unrepentant Franco loyalist, Molina was a signatory to the death warrant by strangling in 1974 of a young anarchist, Salvador Puig Antich, accused of murdering a policeman.
Molina attended a mass in Madrid last November in honour of Franco, alongside the dictator's only daughter, Carmen Franco, 90.