Nielsen previously worked as Kelly's chief of staff at the Department of Homeland Security and then followed him into the White House when he replaced Reince Priebus as Trump's White House chief of staff at the end of July.
Trump said Thursday that Nielsen will need "no on the job training" and will be "ready on Day One".
In a statement, Senator Ron Johnson said, "Ms. Nielsen's long history of service with the Department, her cybersecurity experience and her tenure serving with General John Kelly would serve her well as the next Secretary of the Department of Homeland Security".
Neither the White House nor Nielsen responded to requests for comment.
"I call upon the Senate.to confirm this tremendously qualified and talented nominee", Trump said during a ceremony in the East Room of the White House.
In introducing Nielsen, Trump praised her "sterling reputation" as a longtime public servant dedicated to security, "not politics or ideology".
Elaine Duke has been filling in as acting secretary in the meantime.
Anyone that has had the opportunity to work closely with Ms. Nielsen will agree to the fact that she has always been a no-nonsense player in everything that she does.
Kirstjen Nielsen will be heading the Department of Homeland Security. But Nielsen is not expected to face an especially hard fight, given her background as an experienced professional and a no-nonsense, nonpartisan manager.
Nielsen worked on homeland security issues during stings with the TSA and on the White House Homeland Security Council under George W. Bush.
She would be immediately served a full plate of operational challenges and policy controversies: overseeing the government's response to multiple natural disasters, safeguarding the country's transportation networks from terrorist attacks and protecting its election infrastructure from foreign hackers.
Trump urged the Senate to look at Nielsen's qualifications, calling for a quick confirmation.