"This is a big win for Pennsylvania, for the country, and for anybody who cares about our criminal justice system," said Sen. Pat Toomey (R., Pa.), who led the fight against the nomination.
Some Democrats said Republicans had blocked an accomplished civil rights lawyer who had argued two voting rights cases in the Supreme Court and whose role in the Abu-Jamal case had been distorted.
Obama called the vote "a travesty based on wildly unfair character attacks."
Abu-Jamal is serving a life term for the 1981 killing of Philadelphia police Officer Daniel Faulkner. Initially sentenced to die, he became a worldwide cause célèbre for those who believed he had been railroaded by a racist justice system, while others - including prosecutors, many police organizations, and Faulkner's widow, Maureen - were incensed by his fame.
Senators from the Philadelphia region shied away from supporting Adegbile, who in recent years had helped fight prosecutors' attempts to reinstate Abu-Jamal's death sentence.
Sens. Robert P. Casey Jr. (D., Pa.) and Chris Coons (D., Del.) were among the seven Democrats who opposed the nomination. Senate Majority Leader Harry Reid (D., Nev.) voted "no" for procedural reasons even as he argued for confirmation.
Adegbile, who was not available for comment Wednesday, is the first Obama appointee blocked since November, when Democrats changed Senate rules to require only a majority - not 60 votes - to advance a nomination.
"That the Senate today could not even reach that low bar says a lot about how partisan the administration has become in their second term," U.S. Rep. Mike Fitzpatrick (R., Pa.) said in an interview. He said Maureen Faulkner had personally lobbied senators to oppose the nomination.
Aside from Casey and Coons, Democratic opposition came from senators in conservative-leaning states such as West Virginia and North Dakota, and from incumbents facing difficult reelection fights this fall, such as Mark Pryor of Arkansas and John Walsh of Montana.
Their opposition was the latest evidence that Abu-Jamal's case remains a political flash point.
"It is very hard to defeat a nominee of a sitting president," Toomey said. "It's much harder still if the Senate is controlled by the president's party."
Adegbile was named to head a unit that works to ensure voting rights, enforce laws protecting the disabled, and guard against employer discrimination, among other duties related to civil rights.
The tense debate in the Senate touched on questions of justice, the guarantee of a legal defense for unpopular figures, and the image of a young officer shot in the head as he lay wounded in a Philadelphia street.
Toomey read a searing letter from Maureen Faulkner on the Senate floor.
"The thought that Mr. Adegbile would be rewarded in part for the work he did for my husband's killer is revolting," she wrote. "Please spare my family and me from further pain."
Toomey and Philadelphia District Attorney Seth Williams, a Democrat, said Adegbile was responsible not just for legal work, but for subordinates who attended rallies for Abu-Jamal in what Toomey called efforts "to discredit this country" and its justice system.
Williams said Wednesday that lawyers led by Adegbile took part in Abu-Jamal's "deification."
Adegbile, a teenager when Faulkner was killed, became involved in the case while working at the NAACP's Legal Defense Fund, five years after Abu-Jamal's death sentence had been thrown out but as prosecutors were pushing to reinstate it. The fund filed friend-of-the-court briefs in 2006.
In 2011, when Adegbile was its director of litigation, the NAACP fund took a direct role representing Abu-Jamal. Adegbile told the Senate Judiciary Committee this year that the decision was made by the fund's president.
He said he played only a supervisory role, signing briefs and supervising the work of lawyers in the case. His name appears on three briefs in the case, including two to the Supreme Court.
That court ultimately let stand a ruling sparing Abu-Jamal from death row. With the consent of Maureen Faulkner, Williams reluctantly announced in 2011 that his office would drop its appeals.
Adegbile defended his work on the case in response to senators' written questions, saying lawyers had a duty to vigorously defend even the most unpopular clients.
On Wednesday, some Democrats accused Republicans of creating a caricature of an attorney who had devoted his career to civil rights. Obama said in a news release, "The fact that his nomination was defeated solely based on his legal representation of a defendant runs contrary to a fundamental principle of our system of justice."
Patrick Leahy, (D., Vt.), chairman of the committee, thundered that in 40 years in the Senate he had never seen someone "so misrepresented." Adegbile is senior counsel to Leahy's committee.
Reid read from an Inquirer editorial defending Adegbile, and said Republicans had "distorted this man's good name in an attempt to score points politically." He noted that Chief Justice John G. Roberts Jr., a Republican, once defended a Florida man on death row for killing eight people - and that Democrats had not used that to argue against Roberts' confirmation.
Adegbile's nomination could come back for another vote, but for him to advance, several Democrats would have to change their minds - a prospect Toomey called unlikely.
He said, "This was reasonably decisive."
How They Voted
Voting to confirm Debo Adegbile to head the Justice Department's Civil Rights Division were Sens. Cory Booker (D. N.J.), Tom Carper (D., Del.), and Robert Menendez (D., N.J.).
Voting against were Sens. Robert P. Casey Jr. (D. Pa.), Chris Coons (D., Del.), and Pat Toomey (R., Pa.).