The document states that there will be an increase in co-operation between the two nations.
Afghan security personnel will play a greater role in the planning and undertaking of night time attacks, searches and operations in populated areas, particularly in tribal regions.
It was also announced that an Afghan delegation would participate in the US joint strategic review of policy in relation to Afghanistan being conducted by Holbrooke.
"We understand that President Karzai had written to [US] President Obama last week requesting that Afghanistan be allowed to participate ... President Obama has accepted that request," Macdonald said.
An Afghan delegation headed by the foreign minister was expected to leave Afghanistan for Washington DC within the coming weeks to join the review process.
Macdonald said that the two moves could help Karzai politically "in a big way".
"Karzai has been facing some troubles in recent weeks ... he's been losing some support at home. The new US administration has been making it clear that he is not their favourite person," Macdonald said.
"Obviously, Afghan voters will be very pleased if civilian casualties are reduced.
"And in terms of his international standing, it will obviously help Hamid Karzai if he is involved, engaged with the US administration as it moves forward with its policy in relation to Afghanistan.
"Perhaps we've seen Hamid Karzai rescuing himself politically both domestically and abroad with these two quite important announcements."
The agreements between the two countries come after Karzai told Al Jazeera's Frost Over The World programme that he had not spoken with the new administration in the White House before Holbrooke arrived in the country on Thursday.
He said relations had been poor after he asserted his displeasure at Afghan civilian deaths in US and Nato-led operations.
|The declaration's implementation is to be worked out over the coming days [AFP]
"We are negotiating ... I had to campaign for an end to civilian casualties because we are a sovereign country and the Afghan people expect their government to stand for them," Karzai said.
Sultan Ahmad Baheen, a foreign ministry spokesman, was upbeat about relations between the two sides after the talks at the presidential palace on Saturday.
"The United States of America once again expressed their support for the Afghan government and its people in the fight against terrorism, [support for] development, improving democracy and freedom of human rights," he said.
"And both sides emphasised greater focus in the fight against terrorism and improvement of regional co-operation."
At Sunday's news conference, Holbrooke said that he had carried to Afghanistan a "personal message from President Obama. A message of support for the people of Afghanistan and the democratically elected government of Afghanistan".
Admiral Mike Mullen, the chairman of the US joint chiefs of staff, warned in the Washington Post newspaper on Saturday that the US risks losing its war in Afghanistan because of mounting civilian casualties.
"Until we prove capable ... of safeguarding the population, we will never know a peaceful, prosperous Afghanistan"
Admiral Mike Mullen,
Chairman of the US joint chiefs of staff
"We can send more troops. We can kill or capture all the Taliban and al-Qaeda leaders we can find - and we should," the senior commander at the Pentagon said in the column.
"But until we prove capable - with the help of our allies and Afghan partners - of safeguarding the population, we will never know a peaceful, prosperous Afghanistan.
"Lose the people's trust, and we lose the war."
"You cannot defeat an insurgency this way," Mullen said.
The US has come under increasing criticism over the past few months from Afghans and their leaders over the deaths of civilians during US-led attempts to tackle al-Qaeda and Taliban forces in the country.
Scores of civilians have died during US-led attempts to eradicate opposition fighters in Afghanistan.
Obama is expected to approve the deployment of about 30,000 extra US troops to Afghanistan in the next few days. There is currently 80,000 US and Nato soldiers in the country, backed up by the Afghan army and police.