Local authorities said homes made of adobe collapsed in coastal areas most directly affected by the quake, which struck in the Pacific, 31 kilometers (19 miles) from the seaside town of Acari in the region of Arequipa, according to the US Geological Survey.
"There are two fatalities in the region of Arequipa and so far 65 injured have been reported," General Jorge Chavez, head of the National Civil Defence Institute, said.
Chavez said military planes were delivering humanitarian aid including tents to affected areas.
Peruvian President Pedro Pablo Kuczynski travelled to the region and flew over the quake zone. Speaking to reporters, he attributed the two deaths to adobe houses collapsing.
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The Peruvian navy and the Pacific Tsunami Warning Center in Hawaii ruled out the threat of a tsunami.
Adobe houses were levelled in the coastal town of Lomas and elsewhere in the surrounding area, Santiago Neyra, the mayor of the nearby town of Caraveli said.
Structural damage was reported to a bridge in Arequipa, said the head of the region's highway police, Major Alberto Rojas.
In the city of Arequipa, residents ran into the streets after the quake struck at 4:18 am (local time). It was felt as far away as Lima.
"Here at the clinic the tremor felt super long," a patient in a Lima private hospital told AFP.
The earthquake rocked Peru just before Pope Francis is slated to arrive Thursday for a three-day visit after touring Chile.
The South American country records about 200 earthquakes a year, most of them going unnoticed by the public.
The last major earthquake to shake Peru hit in August 2007, killing 595 people.
A 6.3 magnitude quake was felt in southern Peru on the border with Chile last October, leaving four people with slight injuries.
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