Police closed Spain's main coastal motorway while they hunted for the third device and traffic around the port of Malaga was gridlocked for hours following the explosions.
The first blast was on a beach in Guadalmar at about 1pm (11:00 GMT), and a second device exploded at a tourist marina carpark in Benalmadena Costa two hours later, Spain's interior ministry said.
Eta has previously carried out attacks in vacation areas at this time of year in an effort to disrupt the tourism industry.
In July, Eta set off a series of small bombs in Spain's northern beach resorts of Laredo and Noja, and one in Playa de la Carihuela, a short walk from Benalmadena's marina.
One person was slightly injured in those bombings.
Eta has been fighting since 1968 for an independent Basque homeland in northern Spain and southern France.
The group has been blamed for killing more than 825 people.