Ten-man Panama qualify for Gold Cup
Alberto Zapata scored the only goal in the 31st minute of Tuesday night's match when he sneaked up unmarked to turn in Amilcar Henriquez's free kick.
Panama held on comfortably for three points in the Central American zone Group B match despite having Victor Herrera sent off five minutes before the break when he was given a second yellow card for diving.
Panama finished second in the group behind Costa Rica, who had already qualified.
Guatemala finished bottom but will still have another chance when they play off against Nicaragua for a final place at the CONCACAF Cup, which will be held in the United States in July.