The Aam Aadmi Party said it never promised an investigation into the matter.
A furious Khan also asked the Congress to take back its critical legislative support to the month-old AAP minority government for what he said was a "betrayal" of a promise made by Kejriwal to Muslims in his area.
Kejriwal said at the press conference there would be no probe into the incident as the court has given its verdict and the case has been closed.
AAP leader Sanjay Singh also said there was no mention of the Batla House incident in the party's manifesto for election to the Delhi state assembly.
The drama began when Khan, Congress legislator from Okhla, entered the first-floor room of the Delhi Secretariat where the chief minister and his cabinet colleague Manish Sisodia were briefing the media.
Khan started shouting slogans after Kejriwal denied a probe by a Special Investigation Team (SIT) into the 2008 Batla House shooting.
Khan said Kejriwal had earlier promised an SIT probe, similar to the one the chief minister now wants into the 1984 killings of Sikhs, but was refusing to do so.
Demanding an investigation, Khan called Kejriwal the director of "Radio Jhootistaan" and thundered that he would no longer support the AAP government even if the Congress expelled him.
"I will also request the Congress to withdraw its support to the AAP," he added.
"He (Kejriwal) had promised the people of Okhla that he will probe the Batla House case, and had even distributed hand bills to this effect," the Congress leader said.
He said Kejriwal was now backtracking and "has betrayed the people of Okhla".
The controversial shooting between a Delhi Police team and suspected Indian Mujahideen members broke out in Okhla in September 2008 that left a police officer and two alleged militants dead.
The AAP, which has 28 seats in the Delhi assembly, is in office on the strength of support given by eight members of the Congress. It is also propped up by an Independent and a Janata Dal-United legislator.
Speaking to media persons later, AAP leader Sanjay Singh said: "A plea was filed in the case by Prashant Bhushan, but the court rejected it stating there would be no other plea in the case."
"We should respect the decision of the Supreme Court in the matter," he added.