The order was pronounced on Monday by Chief Metropolitan Magistrate Naveen Kashyap as the main judge hearing the case was absent. The order copy was made available on Tuesday.
The hearing has been scheduled for November 27.
"Taking a lenient view, bailable warrant issued against the accused in the sum of Rs 5,000 and notice to his surety...," the court said.
The court also imposed a cost of Rs 500 on Babbar for his non appearence.
"Taking the lenient view instead of dismissing the present complaint for the reasons of non appearance of the complainant, he is burdened with a cost of Rs 500 to be deposited with DLSA, Central District Tis Hazari Court.
Further, neither the accused nor his counsel is present," the court added.
The court was hearing the criminal defamation complaint filed against Tharoor by Babbar, who has said his religious sentiments were hurt by the Congress leader's statement.
On October 28, 2018, Tharoor, quoting an unnamed Rashtriya Swayamsevak Sangh (RSS) source, launched a sharp attack on Modi likening him with a scorpion sitting on a 'Shivling'.
Speaking about his book "The Paradoxical Prime Minister" at the Bengaluru Literature Festival, Tharoor asserted that the "personality cult of Prime Minister Modi has not gone down well with the RSS and has been a cause of frustration within its ranks".
"There's an extraordinarily striking metaphor expressed by an unnamed RSS source to a journalist, who expressed their frustration to curb Modi - 'Modi is like a scorpion sitting on a 'Shivling'. You can't remove him with your hand and you cannot hit it with a 'chappal' (slipper) either."
The complaint, Babbar had said that Tharoor completely disregarded the sentiments of crores of Shiva devotees by insulting their religious belief.
The complaint was filed under sections 499 and 500 of the Indian Penal Code.
( With inputs from IANS )