The former first lady was scheduled to testify last month but was forced to postpone due to health problems. Clinton fell and suffered a concussion in December. A blood clot was discovered near her brain shortly after.
She faced tough questions by the Senate Foreign Relations Committee and the House Foreign Affairs Committee in her long-awaited congressional testimony. Clinton answered emotionally and fiercely at times, facing off with lawmakers who included potential 2016 presidential rivals.
In her opening statement, Clinton said she takes full responsibility for the department's missteps leading up to the assault at the US consulate.
"As I have said many times, I take responsibility and nobody is more committed to getting this right," Clinton said. "I am determined to leave the State Department and our country safer, stronger, and more secure."
It has been more than four months since Ambassador Chris Stevens and three other Americans were killed in Benghazi.
Clinton went on to say the experience was highly personal for her and for the families of the victims that died.
"I stood next to President Obama as the Marines carried those flag-draped caskets off the plane at Andrews. I put my arms around the mothers and fathers, sisters and brothers, sons and daughters," she told the Senate Foreign Relations Committee at a jam-packed hearing.
The Secretary of State discussed the changes the State Department has made to prevent another attack like Benghazi. Clinton said the department is implementing the 29 recommendations of an independent review board that harshly criticized the department as well as going above and beyond the proposals, with a special focus on high-threat posts.
The review board report faulted "systematic failures and leadership and management deficiencies at senior levels within two bureaus of the State Department" and four employees were put on administrative leave.
Sen. John McCain said he wanted to know if Clinton saw an Aug. 16 cable from the regional security officer who warned the U.S. mission in Benghazi had limited security and might not be able to defend against a coordinated attack.
When asked whether she had seen earlier requests for beefed-up security, Clinton answered: "I did not see these requests. They did not come to me. I did not approve them. I did not deny them."
Her answer provoked a strong response from Sen. Rand Paul, R-Ky, a potential 2016 presidential candidate. If he had been president at the time, Paul said he would have relieved Clinton of her post for not reading the cables from her team in Libya asking for more security.
Other officials also testified that requests for additional security did not reach her level.
Critics accused the administration of security failures leading up to the Sept. 11 attack and being misleading in its accounts, afterwards.
Clinton was questioned regarding the administration's characterization of the attack that followed. The attack was initially characterized as an angry mob that stormed the consulate but was later deemed an organized terrorist attack.
The secretary of state fiercely defended UN Ambassador Susan Rice, who was vilified for widely debunked claims five days after the attack that protests precipitated the raid rather than terrorism. She also stressed her focus on looking ahead to improve security."The fact is we had four dead Americans. Was it because of a protest? Or was it because of guys out for a walk one night who decided they'd go kill some Americans? What difference, at this point, does it make?" Clinton told Sen. Ron Johnson, R-Wis. "It is our job to figure out what happened and do everything we can to prevent it from ever happening again, senator."
After appearing before members of the Senate, the secretary of state answered another round of questions from the House foreign policy panel. Questions were raised before the House Foreign Affairs Committee by Republican members who pressed her on why cables and other memos about security deficiencies in Benghazi seemed to be ignored.
"We just have a disagreement," Clinton told McCain, who dismissed her explanation of events. "We have a disagreement about what did happen and when it happened with respect to explaining the sequence of events."
Clinton is stepping down as secretary of state. Her marathon day on Capitol Hill, Wednesday will probably the last time she'll be appearing before members of Congress as America's top diplomat.
She will appear before lawmakers Thursday to introduce her likely successor, Sen. John Kerry, D-Mass.
The Associated Press contributed to this report.
