Carlos Ascues' fine first-half effort was all Pablo Bengoechea's men needed to edge to victory at the Estadio Alejandro Villanueva.
Bengoechea made numerous changes to the team beaten 3-0 by Chile on Friday, with that loss ending a three-game winning run.
The clash was Guatemala's first since finishing runners-up at the Copa Centroamericana in early September.
Juan Manuel Vargas had the best of the chances in the opening exchanges, firing just wide with his left from an angle.
Guatemala captain Carlos Ruiz went close for the visitors twice around the half-hour mark.
He curled a right-footed, 20-yard free-kick towards the bottom corner that was saved by Pedro Gallese before he headed another chance over.
But Peru went ahead in the 35th minute.
Andre Carrillo played a square pass to Ascues, who fired a powerful 25-yard drive into the bottom corner despite the scratchy surface.
Ruiz was a constant threat to Peru and he had another chance in the 58th minute.
The veteran intercepted a sloppy back pass before surging into the area, but his low left-footed strike was straight at Gallese.
Substitute Irven Avila had an opportunity to seal the win for Peru, only to head well wide of the target from inside the area.
Jonathan Marquez put a long-range effort well wide for Guatemala as they got desperate as the clash went on.
And they were unable to find an equaliser as Peru held on.
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