SAN FRANCISCO — EBay Inc. has failed to knock out a federal antitrust lawsuit over its alleged “handshake” agreement with software developer Intuit Inc. not to poach each other’s employees.

U.S. District Judge Edward Davila in the Northern District of California on Friday denied the company’s motion to dismiss a suit filed last year by the U.S. Justice Department, which accused eBay CEO Meg Whitman of personally striking the no-hire agreement with Intuit’s founder and chairman.