The agreement, which runs through 2009, will take effect Thursday.
The deal, which replaces an interim pact agreed to in December, includes an initial 14 percent pay cut for pilots and assurances the pilots union won't fight any company effort to terminate the pilots' pension.
Judge Adlai Hardin signed the agreement during a hearing in White Plains, N.Y. Earlier in the day, pilots of the Atlanta-based airline, the nation's No. 3 carrier, approved the deal with a vote of 61 percent in favor.
The judge's approval, the last hurdle in the process, came despite an objection filed by the government's pension insurer, which insisted that a $650 million note and $2.1 billion unsecured claim that Delta has promised the pilots should belong to the agency if the pilots' pension is terminated as expected.
Hardin heard arguments from lawyers for both sides, but determined in the end that the agreement was in the best interest of the airline.
It was not immediately clear if the Pension Benefit Guaranty Corp. would appeal.
"It was probably the most significant negotiation transaction we'll face as part of this bankruptcy process," Chief Financial Officer Edward Bastian said of the concessions deal. "It gives us the ability to put the past behind us and make Delta a success again."
Also Wednesday, Delta said in a filing with the bankruptcy court that it lost $27 million in April. Excluding reorganization items, it would have posted a profit of $22 million in the 30-day period. As of April 30, Delta had $2.5 billion of unrestricted cash. It has posted losses of more than $14.4 billion since January 2001.
In a letter to pilots after the pilot vote was made public, Delta's top three executives said the ratification by the rank-and-file marks a new beginning for the airline.
"If we seize this opportunity rather than squander it, Delta Air Lines once again can proudly become the gold standard of the industry," the executives said.
The chairman of the pilot union's executive committee, Lee Moak, said in a statement that the agreement the pilots ratified "provides a framework for Delta to successfully reorganize and emerge from bankruptcy ready to win in today's competitive marketplace."
The cuts are in addition to $1 billion in annual concessions the pilots agreed to in a five-year deal in 2004.
Separately, a retired pilots group had objected to the new deal out of concern the Delta deal would ultimately reduce their benefits based on the pension being terminated. But their objection was resolved at Wednesday's hearing.
As part of the settlement, Delta has agreed to provide retired pilots an administrative claim of $9 million to cover a portion of certain pension benefits that the retired pilots would have gotten since the bankruptcy filing in September had the benefits not been frozen. An administrative claim is a debt incurred by a company that has filed for bankruptcy, with court approval.