After years of battling the growing popularity of the free Linux operating system, software giant Microsoft Corp. yesterday unveiled a dramatic change of course, tossing a lifeline to struggling Linux vendor Novell Inc. of Waltham in the process.

Microsoft and Novell have forged a six-year business alliance in which engineers from the companies will work together to develop software products. In addition, Microsoft will help boost sales of Novell's SUSE Linux operating system, by marketing the software to customers who want to use Linux along with Microsoft's Windows system.

Roger Kay, president of Endpoint Technologies Associates Inc. in Wayland, said the deal could mark a turning point in the fortunes of Novell, which fired its chief executive, Jack Messman, in June, as it struggled to gain market share against rival Red Hat Inc.

"It reminds me a little bit of the deal between Microsoft and Apple," Kay said, referring to Microsoft's decision in 1997 to invest $150 million in a then-moribund Apple Computer Inc. The investment helped launch Apple's rebirth as a major force in computing and consumer electronics.

Linux is the best-known product of the "open source" software movement. While most companies keep their raw computer code a secret, open-source developers publish all the details of their programs, allowing anybody to copy it and make improvements. Open-source programs are usually given away for free by companies that charge for service and support.

Forming an alliance with a Linux vendor is a major shift in strategy for Microsoft.

For years, the company attacked Linux software as a threat to traditional commercial software companies. But Microsoft's business customers have made Linux one of the most popular operating systems for high-end server computers. Kay said the Novell deal reflects Microsoft's acceptance of its customers' desire to use both Windows and Linux in their data centers. "They have now recognized that open source is here to stay, and they have to deal with it in a friendly fashion," Kay said.

Novell shares gained 92 cents, or nearly 16 percent, closing at $6.79. Red Hat lost 2 percent to close at $16.10, while Microsoft slipped four cents to $28.77.

"We have customers who use a mix of technologies to manage their businesses and they demand strong interoperability," said Microsoft chief executive Steve Ballmer. Each year of the alliance, Microsoft will distribute 70,000 coupons good for a year's worth of maintenance and service on Novell's Linux server software.

The deal also addresses the touchy intellectual property issues surrounding Linux. Microsoft has long warned that some Linux features may violate Microsoft patents. But the two companies have reached a royalty agreement that lets each of them use technologies patented by the other. As a result, users of SUSE Linux will be in no danger of patent litigation from Microsoft. Neither will people who develop new software for Linux or other open-source software projects. Microsoft said that it will not enforce its patent rights against such developers.

"This announcement gives our customers interoperability and peace of mind all in one," said Novell chief executive Ron Hovsepian. It also provides a major boost to Novell, the number-two Linux vendor, after North Carolina-based Red Hat Inc.

Shaun Connolly, vice president in the JBoss division of Red Hat, said his company and Microsoft have discussed an alliance similar to Novell's, but nothing came of the talks. "From our standpoint it wasn't anything that was of interest," Connolly said.

The Microsoft-Novell deal could spell trouble for Red Hat. Ballmer said the partnership established Novell as his company's preferred partner in the Linux business, which could slow the momentum of Red Hat, Microsoft's toughest Linux competitor.

"Microsoft is willing to cooperate with Novell, especially if it takes Red Hat down a couple of pegs," said Laura DiDio, a senior analyst for Yankee Group in Boston. Red Hat is already facing a serious threat from database software maker Oracle Corp. which last week said it would begin selling service and support for Red Hat Linux at a much lower price than Red Hat charges.