The Saeed bin Suroor-trained five-year-old won the prestigious race last year and repeated the feat with Belgian jockey Christophe Soumillon, scooping $7.2 million in prize money in one of the world's richest horse races.
Thunder Snow, a 4-1 shot, was locked in a battle with Gronkowski on the final stretch and it was the Godolphin horse that was given the verdict in a photo finish.
The 2-1 favourite Capezzano finished last of the 12 runners.
Thunder Snow's victory was one of four Group One triumphs in a day for Sheikh Mohammed bin Rashid al-Maktoum's Godolphin team.
"It was very hard to get by Gronkowski," Soumillon said.
"I was looking more like a Cheltenham jump jockey in the end instead of an American-style jockey, but you need to keep him going and do something different.
"I want to say a big thank you to Saeed Bin Suroor and Sheikh Mohammed because just before the race they said that I need to be confident and do everything right. Thanks to Thunder Snow as well as without him I wouldn't be able to do such great things."
(Reporting by Hardik Vyas in Bengaluru, editing by Ed Osmond)
