The donation includes $250,000 apiece to the Salvation Army and the Red Cross.
"The destruction that was caused in the wake of Hurricane Irma will have a long-lasting impact on the lives of many," Yankees general partner Jennifer Steinbrenner Swindal said. "During times like these it is important to offer support in whatever way possible, and our hearts go out to all those affected."
New York previously committed $100,000 to Hurricane Harvey relief, and Yankees players pledged $9,000 for every win from Sept. 4 through the end of the MLB season to the ongoing efforts.
The Yankees' three-game series with the Tampa Bay Rays from Monday through Wednesday was played at Citi Field in New York, the home of the New York Mets, rather than Tropicana Field in St. Petersburg, Florida, because of the storm.
Rays manager Kevin Cash said the Trop suffered "minor damages." Longtime Rays third baseman Evan Longoria noted Irma was at the forefront of the players' minds, per Ronald Blum of the Associated Press:
"We watched the Weather Channel nonstop. I'm tired of watching hurricane watch on TV. It's like Anchorman, watching the panda for months and months. I was getting videos, actually actual newscast videos from my neighborhood in St. Petersburg, which is not a good sign. ... I live right on the water, so I was really expecting to come home to a flooded house, and so we got lucky. I had a boat out back that survived. Nothing fell on the house."
AccuWeather founder Dr. Joel N. Myers estimated Irma caused $100 billion in damage.