Shah's deposition started before Judge P B Desai who had last Tuesday summoned him in response to an application filed by Kodnani.
The court had allowed Kodnani's plea to summon Shah and some others as witnesses in her defence in April this year.
On the day of the Naroda Gam riot near Ahmedabad, she said, she had visited the Sola Civil Hospital after attending the Legislative Assembly and was not present at the spot where the violence took place.
Kodnani, who was an MLA in 2002, was made a junior minister in Chief Minister Narendra Modi's government in 2007.
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Three weeks ago, the Supreme Court had asked the SIT court to conclude the trial within four months. A bench headed by then Chief Justice J S Khehar asked the lower court to complete recording of evidence of defence witnesses in two months.
Eleven Muslims were killed in Naroda Gam area on February 28, 2002, a day after the Godhra train incident.
A total of 82 persons are facing trial in the case.
Kodnani has been convicted and sentenced to 28 years in jail in the Naroda Patiya riot case.