"I have longed to die after hearing about the plane crash. I wish I had died and not witnessed such an accident," Hajizadeh told reporters during a press conference in Tehran.
"We accept full responsibility for this act (shooting down the plane), and we will obey and carry out whatever decisions the authorities will make," Hajizadeh was quoted as saying by the official IRNA news agency.
The Iranian commander said that since Iran was on "high alert" on Wednesday because of the US threats of hitting 52 spots in the country, the operator of the missile launch site was concerned about a possible "US cruise missile", Xinhua reported.
The passenger plane was mistaken for a "US cruise missile", Hajizadeh said, adding that the missile operator also encountered some communication problems and "he made a bad decision, triggered the missile and hit the plane".
On Wednesday, a Ukrainian Boeing 737 passenger plane crashed near Tehran, killing all 176 people onboard.
Iran's armed forces on Saturday admitted that the Ukrainian plane was "unintentionally" hit by Iran for which "human error" was to blame.