The death of Alexis, 34, of Fort Worth, Texas, brought the toll of the carnage at the Navy Sea Systems Command headquarters to 13. Officials said at least a dozen others were injured.
The shooter's identity was confirmed based on a partial finger print analysis, authorities said.
Valerie Parlave, assistant director in charge of the FBI's Washington D.C. field office, said investigators are trying to learn everything they can about Alexis.
She asked anyone with information about his recent movements, contacts and associates to contact the FBI at 1-800-CALL-FBI.
More than eight hours after the shooting, Metropolitan Police Chief Cathy Lanier said the scene remains active as authorities search for a man who is considered to be a "potential" shooter.
The man being sought was described as a black man in his 50s wearing an olive drab uniform and carrying a long gun.
Another man who was sought for a possible connection to the shooting was located this afternoon and was no longer a "suspect or person of interest, " according to a tweet from the Metropolitan Police Department.
Lanier declined to discuss what evidence led police to believe the massacre could have potentially been carried out by more than one person.
"We have reason to believe these people may be involved and we want to talk to them," Lanier said at an afternoon news conference. She said there was "no known motive" for the massacre.
Among the wounded was a law enforcement officer who was shot in an exchange with the gunman.
"I think the actions by the police officers, without question, helped to reduce the number of lives lost," Lanier said.
The shooting has brought parts of Washington D.C. to a standstill as authorities assessed the situation.
The Washington Nationals, whose stadium is a couple blocks away from the Naval Sea Systems Command headquarters, said the team's game tonight against the Atlanta Braves will be postponed until Tuesday.
The Senate complex was placed under a precautionary lockdown this afternoon "in light of the uncertainty surrounding the shooting" and the possibliity that a second shooter may be at large, Terrance W. Gainer, Senate Sergeant at Arms, wrote in a note to the Senate community.
At nearby Reagan National Airport this morning, a ground stop was imposed by the FAA. All planes have since resumed flying out of the airport, a Metropolitan Washington Airports Authority spokeswoman told ABC News.
Nine D.C. public schools were placed on lockdowns this morning, according to the District of Columbia Public Schools' Twitter account, however all schools were dismissed as scheduled this afternoon.
Washington D.C. Congresswoman Eleanor Holmes Norton told reporters the district has not "had a day like this since 9/11."
President Obama said he has been briefed on the situation and spoke about the shooting at the beginning of a news conference.
"We are confronting yet another mass shooting, and today it happened on a military installation in our nation's capital," he said.
Obama said he wanted a "seamless" investigation into the shooting and is standing with the victims and their families affected by what he called a "cowardly act."
"It targeted our military and civilian personnel, men and women who were going to work, doing their job protecting all of us. They are patriots and they know the dangers of serving abroad," Obama said. "But today they faced the unimaginable violence that they won't have expected here at home."
Two law enforcement officers were among the injured when the suspect fired shots inside the 3,000-person building at 8:20 a.m. Law enforcement officials initially told personnel to evacuate the building but they were later told to shelter in place.
A spokesman for the Bureau of Alcohol, Tobacco, Firearms and Explosives sent a team of special agents to help secure the scene. This is the same team that helped apprehend Boston Marathon bombing suspect Dzhokhar Tsarnaev, according to the spokesman.
Three gunshot victims were taken to Washington Medical Center with "severe injuries," according to Janis Orlowski, chief medical officer at the hospital.
The victims were described as a male Metropolitan police officer who had "multiple gunshot wounds to his legs," a woman who was shot in the head and the hand and another woman who was shot in the shoulder.
Orlowski said all three are in critical condition, however they are conscious and are expected to survive.
She said the hospital is expecting to receive more victims, but she was not sure how many.
Patricia Ward, a logistics management specialist at the Navy Yard, said she heard a series of shots, at least seven, in rapid succession.
"A few of us just ran outside the side exit," Ward said.
Outside the building she saw a security guard with her gun drawn who told them to run and shelter.
Ward said the building has security.
"You need a car to enter the building. It's very hard to get in without a card," she said.
"Being with the incident that happened today, not secure enough for me," Ward said.
Frank Putzo, an attorney at the Navy Yard, told ABC News affiliate WJLA he was on the fourth floor of the building when the shooting began.
"We heard three sounds, it sounded like a table collapsing on the ground," he said.
He said he came out of his office and heard a "very loud pop" about a minute later that he estimated was about 100 feet away.
"When that happened everyone said, 'This is no drill, go, go, go,'" he said. "And a whole bunch of us were able to make it to the emergency exits. And we heard several more shots."
The Naval Sea Systems Command, the largest of the Navy's five commands, is responsible for engineering, building, buying and maintaining ships, submarines and combat systems in the Navy's fleet.