Lou Fintor, a spokesman for the US embassy in Pakistan, said: "He [Holbrooke] is in Pakistan to listen and learn the ground realities of this critically important country. This was the focus of his discussions."
He was referring to Holbrooke's talks on Tuesday with Zardari, General Ashfaq Kayani, the army chief, and other high-level political and security officials.
Holbrooke's appearance in Peshawar, the main city in Pakistan's northwest, was overshadowed by the death of a secular politician and six other people in a bomb attack on Wednesday.
Police said it appeared the bomb was hidden in a motorcycle and was detonated by remote control when a vehicle carrying Alam Zeb Khan passed.
The blast wounded the Awami National Party legislator, his bodyguard, two of his staff and three passers-by, a police officer said.
Khan later died at a hospital.
Obama phone call
Meanwhile, Obama and Zardari agreed in their phone call "to start an active engagement for the resolution of problems facing our region through a holistic strategy", Pakistan's foreign ministry said in a statement.
Obama reiterated his support for democracy, socio-economic and human development in Pakistan, the ministry added.
The call came a day after the White House said that Obama had ordered an inter-agency review to examine US policy on Pakistan and Afghanistan before a Nato summit in April.
There are 37,000 US forces in Afghanistan at present, as part of a western military presence of about 70,000 troops.
And the US military has drawn up plans that could increase the number of US troops there to about 60,000.
Obama said this week that there was no doubt "terrorists" were operating in havens in the tribal regions of Pakistan and the US wanted to make sure Islamabad was a strong ally in fighting that threat.
Fintor, the US embassy spokesman, said Holbrooke would report his Pakistan findings to Obama and Hillary Clinton, the US secretary of state, after he visits Afghanistan and India in the coming days.