Aldana, 63, still had appeal avenues available to her but after initially vowing on Twitter to "continue in the fight to transform this country," her party later said she would abandon the legal challenges to her ban.
The Constitutional Court had rejected an appeal by the small center-left Semilla Movement party against an Electoral Court decision, subsequently upheld by the Supreme Court, to bar Aldana from standing.
She was running third in polls ahead of the June 16 vote.
She had been barred after she was accused in March of the irregular purchase of a building for the public ministry and the creation of fake jobs during her tenure as public prosecutor.
As public prosecutor, Aldana joined the UN-affiliated International Commission Against Impunity in Guatemala in bringing down a deeply ingrained customs bribery structure aimed at avoiding taxes, which in 2015 provoked the resignation and arrest of former president Otto Perez over corruption allegations. He remains in prison.
During her tenure from 2014-18, dozens of senior officials, businessmen, lawmakers and individuals were jailed for alleged acts of corruption.
Aldana said the accusations were aimed at punishing her for fighting corruption in Guatemala.
"It has become clear that the fight against corruption and criminal structures in our country has a high cost for those, like me, who decide to do it," she wrote on Twitter.
Her running mate, Jonathan Menkos, told a press conference that those responsible for corruption in the country were the ones opposed to Aldana's candidacy.
"Of course our aim is to end corruption," he said, adding that the party would now concentrate on winning seats in congress and town halls.
Menkos said Aldana would, for safety reasons, remain in El Salvador, where she has been since March 19, the day before a judge ordered her arrest.