A Georgia publisher, outbidding three major communications companies, has agreed to buy the two daily newspapers in Jacksonville, Fla., from CSX Corp. for about $200 million, apparently the highest price ever paid for a newspaper acquisition.

William S. Morris III, chairman of the family-owned Morris Communications Corp. and publisher of the Augusta Chronicle and Herald, will acquire the Florida Times-Union and the Jacksonville Journal.

The two profitable dailies dominate the growing North Florida-South Georgia market with a combined daily circulation of 204,000. Included in the deal are a small daily paper in St. Augustine, a weekly in Crescent City, and the Jacksonville papers' commercial printing operations.

No price was announced, but CSX, the Norfolk-based railroad formed last year by a merger of the Chessie System and Seabord Coast Line, said it would yield an after-tax return of $2.50 to $3 a share, which industry analysts said indicated a price of $190 million to $200 million.

That far outstrips the $105.6 million price paid by Times-Mirror Corp., parent of the Los Angeles Times, to acquire the Hartford Courant in 1979, or the $95 million it paid for the Denver Post a year later. Time Inc., last owner of the defunct Washington Star, paid $20 million for it in 1978.

CSX confirmed that Morris outbid the Gannett Co. Inc., Cox Newspapers of Atlanta and Capital Cities Communications Inc. "It's unusual for anybody to outbid Gannett," said Bruce Thorpe, an analyst with Jones, Lynch & Ryan. "It's a lot of money. But then every acquisition in the past few years has seemed like a lot. It's a good property in a solid market."

CSX sought a buyer because it does not wish to be in the newspaper business, according to Ed Ebel, vice president for corporate communications. He said Seaboard had owned the Jacksonville papers "probably since the turn of the century," but CSX wants to concentrate on its "main business interests, namely transportation and natural resources."

The Jacksonville papers will be the largest in Morris' chain, which also owns dailies in Savannah and Athens, Ga., and Amarillo and Lubbock, Tex., and five weekly papers.