The European Union executive said in a statement it was certain "Microsoft will now take the necessary steps to comply with its obligations under the Commission's 2004 decision."
Microsoft, which was fined 280.5 million euros ($400.6 million) in 2006 for failing to comply, faced the prospect of steep new fines if it did not accommodate the Commission.
Among other reversals, Microsoft will make available to so-called "open source" software developers information they need so their programs work smoothly with Microsoft's Windows operating system for personal computers.
Microsoft has also sliced high royalties for interoperability information, the Commission said.
Microsoft suffered a decisive defeat in September when the Court of First Instance in Luxembourg upheld the ruling that the world's largest software maker had abused its dominant market position to crush rivals. It upheld the Commission on all major points, including a 497 million euro fine.
Among other things, the court upheld the Commission's finding that Microsoft failed to give rivals enough information so their work group server software would work as smoothly with Microsoft's desktop computers as Microsoft's own software.
The Commission said Microsoft had made substantial changes to its royalty program in three ways.
First, open source software developers will be able to access and use the interoperability information.
Second, the royalties payable for this information will be reduced to a nominal one-off payment of 10,000 euros.
Third, the royalties for a worldwide license including patents will be reduced from 5.95 percent to 0.4 percent.
Microsoft's new stance was signaled earlier this month, when the company withdrew from an appeal against a South Korean antitrust ruling. It had appealed to the Seoul High Court.