Abizaid escaped unscathed from an attack by rocket-propelled grenades (RPG) in the flashpoint Iraqi town on Thursday, a US military official said.
Brigadier-General Mark Kimmitt said the RPGs were launched as Abizaid and Major-General Charles Swannack, commander of the 82nd Airborne Division, travelled in a convoy in Falluja, west of the capital.
"Three rocket-propelled grenades were fired at their convoy from the rooftops in the vicinity," Kimmitt, the deputy operations chief for the US-led occupation forces said in Baghdad.
Two civilians were killed and an undisclosed number wounded in the shootout, Aljazeera's correspondent reported.
Following the attack, Abizaid cancelled his tour of Falluja and returned to a nearby US base, the correspondent said.
Abizaid is the third high-profile US official to escape an attack in Iraq.
The others are US administrator Paul Bremer, whose convoy was attacked in December, and Deputy Defence Secretary Paul Wolfowitz, whose Baghdad hotel was hit by rockets.