The purchase, expected to be completed June 1, is Japan's largest-ever real estate transaction.
"This transaction highlights Morgan Stanley's continued long-term commitment to investing in Japan and optimistic outlook for the nation's economy and hotel industry," Morgan Stanley said in a statement.
The investment bank already has interests in 14 Japanese hotels.
All Nippon, also known as Zennikku or ANA, said it would determine how much profit the sale would generate in the fiscal year ending March 2008.
It also said the sale -- which includes the ANA InterContinental Tokyo and resort hotels on the southern Japanese island of Okinawa -- was in line with its strategy of focusing on passenger and cargo flight operations.
ANA is Japan's second-largest domestic and international carrier after Japan Airlines Corp.
The 13 hotels will be operated by a joint venture launched by ANA and Intercontinental Hotels Group PLC last year, the companies said.