On his first visit to the country, Mr Howard told a joint news conference with President Karzai that Australian troops would stay in both Afghanistan and Iraq until the "missions are completed". He gave no details of a timeframe.
He also spoke of Afghanistan's fight against the narcotics trade.
In recent years the central Asian country has been the biggest producer of opium and its derivatives morphine and heroin.
"In our discussion, we have recognised the challenge of the narcotics trade in your country which is the source of concern to many in the West, but we are with you in the fight against terrorism and we remain committed with other coalition partners to contribute to the strengthening of your country," he said.
As a strong supporter of the United States, Australia sent troops to Afghanistan in late 2001 as part of the campaign to oust the Taliban regime and hunt for al Qaeda militants after the September 11 attacks on the United States.
One Australian soldier was killed in Afghanistan in February 2002, while nearly 60 foreign troops, most of them Americans, have been killed in the Taliban-led insurgency this year, one of the bloodiest periods since Taliban's ouster.
Australia has about 200 combat troops in Afghanistan. The government is due to decide within weeks whether to send a military reconstruction team to the country.
Flying Visit
During a flying two- hour visit to troops in southern Afghanistan, Mr Howard told them no nation has the right to take the bravery and professionalism of its fighting men and women for granted.
He said there is strong support in Australia for what they are doing.
Australia’s contribution to provincial reconstruction teams work under a US-led civil-military program to help reconstruction and security.
A primary goal is also to extend the influence of Mr Karzai's Government beyond the capital Kabul.
"There are two challenges: the military challenge and helping rebuilding.
They're both quite important, that's why we're considering a PRT force," Mr Howard said.
"The best thing Australia can do in both Iraq and Afghanistan is to stand till the missions in which it is involved in these countries are completed," Mr Howard also visited lauded Afghanistan's efforts to establish democracy and its fight against terrorism.
"I'd like to thank you for bringing openness and democracy to this country.
It's a long and difficult struggle," he said.
"We have a common interest in fighting terrorism. I respect your courage. It's not easy. You're in the front line in the fight against terrorism, and we're with you in this fight."
President Karzai says the international effort to stabilise his country will also contribute to stability in Australia and encouraged Australia to send more troops to help rebuild his country.
"The stability of Afghanistan will eventually be stability and peace in Australia," he said.
On to Pakistan
After his whirlwind tour of Afghanistan, Mr Howard flew into Islamabad for talks with Pakistani leaders on cooperation in the aftermath of last month's devastating earthquake.
During his three-day stay, Mr Howard's was to meet President Pervez Musharraf and Prime Minister Shaukat Aziz and visit quake-hit areas, foreign ministry spokeswoman Tasnim Aslam said.
"The visit is aimed at further strengthening the multi-faceted relationship between the two countries," she said.
Australia has announced a total contribution of $14 million for quake relief operations, channelled through UN agencies and Australian non-governmental organisations.
At least 74,000 people died and three and a half million were left homeless on October 8, when the 7.6 magnitude earthquake struck Pakistan’s northern regions and the Pakistan administered part of Kashmir.
Pakistan and Australia were also expected to sign agreements on cooperation in agriculture, natural gas exploration and higher education, Ms Aslam said.