Hopes of finding survivors were slim as sea rescue teams searched the waters off El Hierro, an island in the Atlantic archipelago.
It is the latest in a series of such disasters off the coast of Africa.
“The search operation is resuming,” Spain’s maritime rescue organisation told AFP.
The 48 are “presumed dead”, Canaries regional president Fernando Clavijo told journalists on Saturday night.
More bodies will likely appear “over the next two, three days”, washed up by the current, he added.
Twenty-seven migrants were rescued and nine bodies recovered after the boat, which had set out from Nouadhibou in Mauritania, some 800 kilometres (nearly 500 miles) away, overturned off El Hierro.
The tragedy hit when rescuers arrived to assist the migrants after they themselves called emergency services, Spanish officials said.
Migrants rushed to one side of the precarious boat, causing it to tip.
The migrants “had gone two days without food or water”, which may have fuelled their panic, Anselmo Pestana, head of the Canary Islands prefecture, told journalists in the port of La Estaca.
Spanish government sources said the boat may have been carrying up to 90 people, instead of 84 as originally announced, which could put the number of missing at more than 50.
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This disaster follows the death of 39 migrants in early September when their boat sank off Senegal while attempting a similar crossing to the Canaries, from where migrants hope to reach mainland Europe.
Thousands of migrants have died in recent years setting off from west Africa to reach Europe via the Atlantic aboard overcrowded and often dilapidated boats.