He was sent to the ED custody till August 14 by a Delhi court after he was flown in here from Srinagar.
A senior official in the central probe agency said Wani (36) was arrested in the morning by the ED with the help of the state police.
The ED had recently got a non-bailable warrant (NBW) issued against him from a Delhi court.
"The warrant against Wani was executed and he will now be confronted with Shah and others in order to take the probe forward," he said.
The agency also questioned Shah's wife, Bilquees, in connection with the case yesterday.
She has been summoned again by the agency later this week and has been asked to furnish certain financial documents.
Shah, now in the ED custody, was arrested by the agency from Srinagar on July 26.
The ED action against Shah and Wani is in pursuance of an August 2005 case, wherein the Delhi Police's Special Cell had arrested Wani, an alleged hawala dealer, who had claimed that he passed on Rs 2.25 crore to Shah.
Wani was arrested allegedly with Rs 63 lakh, received through 'hawala' channels from the Middle East, and a large cache of ammunition, on August 26, 2005.
During questioning, he had told the police that Rs 50 lakh was to be delivered to Shah and Rs 10 lakh to Jaish-e- Mohammad area commander in Srinagar, Abu Baqar, and that the rest was his commission.
Wani, who hails from Srinagar, had also claimed that he delivered around Rs 2.25 crore to Shah and his kin in multiple instalments over the past year.
The ED, sources said, wants to probe the "proceeds of crime" of alleged terror financing in this case.
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