"It's important to facilitate access to all women, irrespective of their place of residence, as it is important to take this pill in the 72 hours after sexual relations," said Health Minister Trinidad Jimenez.
Pharmacies are now able to sell the morning-after pill to persons of any age. The contraceptive has hitherto been available only on prescription.
She said the move would "avoid unwanted pregnancies" but warned it "must not be used as a habitual method of contraception."
The government announced the move last May, noting that other countries which have allowed over-the-counter sales of the pill, including France, Britain and the United States, had seen a "significant" drop in the number of unwanted pregnancies.
The number of abortions in Spain doubled between 1998 and 2007, according to health ministry figures.
Spain's Socialist government on Saturday approved reforms to the country's abortion law, despite strong opposition from the Roman Catholic Church.
Under the new measures, abortions would be allowed for women of 16 and over without their parents' consent up to the 14th week of pregnancy, and up to 22 weeks if there is a risk to the mother's health or if the foetus is deformed.
Women can also undergo the procedure after 22 weeks if the foetus has a serious or incurable illness.
Spain decriminalised abortion in 1985, a decade after the death of right-wing dictator Francisco Franco, but only for cases of rape, fetal malformation and when a pregnant woman's mental or physical health is deemed to be at risk if the pregnancy goes to term.