The newspaper La Hora reported President Otto Perez Molina said 39 of the fatalities were in San Marcos, eight in Quetzaltenango and one in Solola.
San Marcos Gov. Luis Rivera said earlier another 155 people had been injured. The newspaper said the number of people reported missing had declined from 100 to 23.
Dozens of homes had been damaged or destroyed in Nahuala.
Both temblors hit near the border between Guatemala and Mexico, CNN reported.
The earlier quake was felt as far away as Mexico City. The second shaker measured about a magnitude-5.
While the president said the number of people without electricity had been reduced from 166,000 to 26,000, La Hora said the power company Energuate said at least 266,000 people were without service in San Marcos.
The first quake was the strongest in the country since 1976, when an earthquake measuring 7.5 on the Richter scale killed 23,000 people.
Quakes in the magnitude-7 range are considered major while those between 5 and 5.9 are moderate. The second quake hit just before 3 p.m., 3 hours after the first and was centered about 10 miles to the south-southwest.
A minor tsunami in the Pacific Ocean was reported by the United Nations agency UNESCO, but there had been no reports of excessive wave activity or damage in other areas.