Defense Secretary Austin also told Iraqi Prime Minister Mohammed Shia al-Sudani that US troops were "ready to remain" in the country at Baghdad's invitation, a thorny issue that has divided public opinion in both countries.
The visit, which had not been publicly announced in advance, comes ahead of the March 20 anniversary of the ground invasion that started two decades of bloodshed which Iraq is only now beginning to exit.
"I am optimistic about the future of our partnership," Austin told reporters in Baghdad after meetings with Sudani and Iraqi Defence Minister Thabet al-Abbasi.
"The United States will continue to strengthen and broaden out partnership in support of Iraqi security, stability and sovereignty."
The Iraqi premier told Austin he also wanted to "strengthen and consolidate relations" with Washington, and underlined Baghdad's commitment to "maintaining balanced relations with the regional and international powers".
Since US-led coalition troops ousted Saddam's Sunni Arab-dominated regime in 2003, Iraq's Shiite majority has led Iraq under a confessional power-sharing system.
Successive governments have forged close ties with Iraq's Shiite-led neighbour Iran, the arch foe of the United States, in a delicate balancing act for Baghdad.
Both Washington and Tehran provided extensive support during Iraq's fightback against the Sunni extremists of the Islamic State group, who overran swathes of northern and western Iraq in 2014.
The jihadists were ousted from Iraqi territory in 2017 but retain sleeper cells in desert and mountain hideouts in both Iraq and neighbouring Syria.
- 'Vital work' -
Iraq announced the end of combat operations by US-led coalition forces in late 2021 but some 2,500 American non-combat troops remain deployed to provide advice and training.
"We must be able to operate safely and securely to continue this vital work," Austin said.
In recent years, bases hosting coalition forces have come under drone and rocket attacks blamed on pro-Iranian factions.
The Pentagon chief thanked Sudani and Abassi for "their commitment to ensure that the coalition forces in Iraq... will be protected from state and non-state actors".
Austin's visit comes after he held talks in neighbouring Jordan with King Abdullah II, a staunch US ally in the region.
While there, Austin voiced "his concerns on a range of shared challenges, including... maintaining focus on security and stability in Iraq, and countering other destabilising activities in the region," a Pentagon statement said.
Austin also visited Iraq's Kurdistan, meeting with the autonomous northern region's president Nechirvan Barzani, a US ally, in the regional capital Arbil.
"For the country of Iraq to realize its full potential, Erbil (Arbil) and Baghdad must work together for the good of all Iraqis," said Austin.
Barzani thanked the United States for "its continued support to Iraq and Kurdistan; we have common interests with the US in maintaining the security and stability of Iraq."
Despite its vast oil and gas reserves, Iraq has suffered from decades of underinvestment in its infrastructure and public services that have sparked repeated waves of protests.
October 2021 elections were followed by a whole year of political vacuum before Sudani was sworn in at the head of a government led by pro-Iran factions.
The political arm of Iraq's Hashed al-Shaabi (Popular Mobilisation) force, made up heavily of Tehran-trained groups, has long demanded the departure of all remaining coalition troops, although its calls have been less shrill since it entered government.
There had been a sharp deterioration in US-Iraqi ties under the Donald Trump administration following the assassination of Iran's foreign operations chief General Qasem Soleimani along with his Iraqi lieutenant, Hashed number two Abu Mahdi al-Muhandis, in a drone strike at Baghdad airport in January 2020.
In the run-up to the invasion anniversary, Iraq has hosted a raft of foreign officials, including UN chief Antonio Guterres and the Iranian, Russian and Saudi foreign ministers.
German Foreign Minister Annalena Baerbock began a four-day visit Tuesday and was received in Baghdad by her Iraqi counterpart Fuad Hussein.
"IS remains a threat. That's why German soldiers are here... as part of the anti-IS coalition and the NATO mission," she told a news conference.
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