He said he was "honored to serve President-elect Obama."
Gates' appointment fulfilled a campaign promise by Obama, the naming of a Republican to his Cabinet.
Holder vowed to revitalize a Justice Department staggered by scandal during the Bush administration, both over the dismissal of federal prosecutors and the administration's program of wiretapping as part of its war against terrorists.
Napolitano, like Clinton, must resign her current job. As a border state governor, she has experience with immigration issues, one of the pressing concerns that will confront the new administration.
Obama said Jones, his national security adviser, "will bring to the job the dual experience of serving in uniform and as a diplomat. He has commanded a platoon in battle, served as supreme allied commander in a time of war and worked on behalf of peace in the Middle East."
The event was unlike those of last week, when Obama was the only one to speak. This time, he called on each of his appointees to make remarks, beginning with Clinton.
Vice President-elect Joe Biden said each member of the team shares the goals and the principles of the new administration that "strength and wisdom must go hand in hand," and that America's security "is not a partisan issue."
Obama has settled on additional members of his Cabinet, although they have not yet been announced.
Among them are former Senate Democratic leader Tom Daschle to be his secretary of health and human services and New Mexico Gov. Bill Richardson to be commerce secretary.
Secretary of State Condoleezza Rice, asked about Clinton at a news conference in London, said Monday: "I think that she will bring enormous energy and intellect and skill to the position."
"Most important, I know her to be somebody who has what you need most in this job, which is a deep love for the United States of America," Rice said. She added, "As to advice, I'll give her that advice privately, and then she won't - and you won't - hear from me again."
The decisions mean Obama has half of the 15-member Cabinet assembled less than a month after the election, including the most prominent positions at State, Justice, Treasury and Defense. With the world grappling with war, recession and terrorist threats that erupted this week during coordinated attacks in India, Obama was moving swiftly to try to bring reassurance and continuity in the federal government when he takes over in less than two months.
Clinton's nomination is the latest chapter in what began as a bitter rivalry for the Democratic presidential nomination. To make it possible for his wife to become secretary of state, party officials said, former President Bill Clinton agreed to:
_Disclose the names of every contributor to his foundation since its inception in 1997 and all contributors going forward.
_Refuse donations from foreign governments to the Clinton Global Initiative, his annual charitable conference.
_Cease holding CGI meetings overseas.
_Volunteer to step away from day-to-day management of the foundation while his wife is secretary of state.
_Submit his speaking schedule to review by the State Department and White House counsel.
_Submit any new sources of income to a similar ethical review.
Sen. Richard G. Lugar of Indiana, the top Republican on the Senate Foreign Relations Committee, said Sunday on ABC's "This Week" that he plans to vote to confirm Clinton.
Lugar said there would still be "legitimate questions" raised about the former president's extensive international involvement. "I don't know how, given all of our ethics standards now, anyone quite measures up to this who has such cosmic ties, but ... hopefully, this team of rivals will work," Lugar said.