The purported witness, Ali Abbas, said this on Sunday in a telephone call to Aljazeera's programme The Iraqi Scene.
Late on Wednesday, a US air force F-16 launched two 227kg bombs, one laser-guided and one GPS-guided, at al-Zarqawi's house near the city of Baquba, northeast of Baghdad.
Also on Sunday, the top US commander in Iraq, General George Casey, rejected the account of a person circulated by wire services that US soldiers assaulted al-Zarqawi when they found him alive after the air strike, calling it "baloney".
Casey said al-Zarqawi died when US soldiers were trying to save his life inside an ambulance.
The US military is yet to release its autopsy report on al-Zarqawi. Casey said officials were awaiting the results of a DNA test.
The examination by two US military forensic specialists flown in specially for the autopsy was part of an investigation to reconstruct the last minutes of al-Zarqawi's life.
US commanders initially said he died in the air strike but later said he survived and died soon after.
An Iraqi man on Saturday raised questions about al-Zarqawi's death, telling AP Television News he saw US soldiers after the air strike beating an injured man who resembled the dead Sunni fighter until blood flowed from his nose.
Casey told Fox News on Sunday that after the allegation was made, the military had "already gone back, looked at it".
The rubble of al-Zarqawi's house
near Hibhib outside Baquba
"Our soldiers who came on the scene found him being put in an ambulance by Iraqi police. They took him off, rendered first aid, and he expired," Casey said. "And so he died while American soldiers were attempting to save his life. And so the idea that there were people there beating him is just ludicrous."
The Iraqi witness, identified only as Muhammad, said he lives near the house where al-Zarqawi and five others were killed. He said residents put a bearded man in an ambulance before US soldiers arrived. A similar account appeared in The Washington Post.
US officials previously said al-Zarqawi mumbled and tried to roll off a stretcher before dying at the bombed house in Hibhib, outside Baquba.
Because of the confusion over the sequence of events following the bombing, the military has promised to release a chronology.
In addition to al-Zarqawi, the air strike killed two men, two women and a young girl who were in the house, the US command says.
At least one US officer said American troops responded quickly, while a senior Iraqi official said on Sunday that they may have arrived as much as an hour after the attack.
"After the national Iraqi police arrived to the scene and got the injured, got the dead sorted out. In an hour or so, I think, coalition forces have arrived to the scene also to help in the logistics of the operation afterwards," Mouwafak al-Rubaie, Iraqi's national security adviser, told CNN.
Al-Rubaie said troops combing though the debris found al-Zarqawi's diaries, telephone numbers, computers and a database in one computer.