President Jimmy Morales received 50,000 quetzals ($6,808) each month as a 'Bonus for Extraordinary Responsibility' from the Defense Ministry that was not part of the official presidential salary, Guatemala's federal auditor said last month.
With the bonus, which began last December, Morales' monthly pay package totaled about 200,000 quetzals ($27,233), according to the defense minister. He later returned the bonus funds.
The court's decision preserves Morales' immunity against corruption investigations. In a separate case last month, Guatemala's Congress voted to protect the president from a potential probe into alleged illegal campaign financing.
'The president already returned the bonus and ... a person cannot be judged twice for the same incident. That is what causes it to be rejected,' Supreme Court spokesman Angel Pineda said of the bonus case.
A statement from the president's office said Morales accepted the court's decision, and contended that actions against him had been politically motivated.
Guatemala's federal prosecutor and a United Nations-backed commission against impunity in Guatemala (CICIG) had pushed to revoke immunity for Morales after his salary bonus became known.
Last month, thousands of Guatemalans marched to protest high-level corruption in the impoverished country and to demand that Morales and Guatemalan lawmakers step down.
The federal auditor, which audits all government spending, said on Sept. 12 it would investigate the salary bonus, but has not yet produced any findings.
With the salary bonus, Morales earned 70 percent more than Chilean President Michelle Bachelet and 130 percent more than Mexican President Enrique Pena Nieto, two of the region's best-paid leaders.
The bonus made his salary about 90 times more than the $300 monthly minimum wage in Guatemala, where 60 percent of the population lives in poverty.