While the 17-minute recording has not been fully authenticated as featuring the voice of al-Zawahri, it was posted by as-Sahab, al-Qaeda's media wing.
The voice is similar to that featured on previous authenticated statements.
The United Nations has estimated that at least 200,000 people have died in Darfur since 2003, when Arab fighters alleged to have links to the government in Khartoum began a series of attacks against black civilians.
Zawahri dismissed the ICC's decision to issue war crimes and crimes against humanity charges against al-Bashir, calling the move a Western plan to interfere in Sudan.
"I am not defending Omar al-Bashir or his regime, nor am I defending what it has done in Darfur and elsewhere," he said.
"The issue isn't one of Darfur and solving its problems. It is about finding an excuse for more foreign interference in the Muslim countries in the framework of the contemporary crusader-Zionist campaign," Zawahri said on the audio recording.
Al-Zawahri also criticised the United Nations for what he called its failure to protect Palestinians during Israel's recent 22-day war on Gaza, drawing comparisons with the world body's response to the situation in Darfur.
"Why hasn't the United Nations moved to protect the Palestinians in Gaza from Israeli barbarity and criminality, while it pretends to cry over the suffering of the people of Darfur?" he said.
"Why hasn't the United Nations and the international community intervened to lift the siege from Gaza, while it pretends to cry over the people of Darfur being deprived of relief and aid?"
The al-Qaeda deputy also demanded that Western leaders including George Bush, a former US president, and Vladimir Putin, Russia's prime minister, be put on trial.