In introducing Gates, Obama said, "I will be giving Secretary Gates and our military a new mission as soon as I take office: responsibly ending the war in Iraq through a successful transition to Iraqi control."
Obama also indicated that he would act on his campaign promise to boost troop levels in Afghanistan, where the Taliban has been steadily growing stronger.
"As Bob [Gates] said not too long ago, Afghanistan is where the war on terror began, and it is where it must end," Obama said.
Despite the apparent differences in the Obama national security team, there is also a streak of pragmatism.
Gates is known for being results oriented, nonideological and a low-key conciliator.
"I think the fact that he is going to agree to do this, serve two presidents who are polar opposites in ideology, especially polar opposites on the war, show that he has the ability to help that along," said former GOP stragegist and now an ABC News consultant Matthew Dowd.
Jones, a retired Marine general, is the former commander of NATO forces.
"He seems to be a guy who functions well, makes the trains run on time, that gets the job done, that doesn't bully people, doesn't push people around, is not overly emotional," Dowd said.
Under Rice, the U.N. ambassador post will be elevated to a Cabinet rank as it was in President Clinton's administration, giving her a direct line to the president. Bush had downgraded the post.
ABC News' Eileen Murphy contributed to this report.