A senior US state department official said earlier that Clinton, in her calls, raised the prospect that US legislators could back away from US economic aid for Pakistan because of the turmoil.
Pakistan's decision was "a first step of what has to be an ongoing reconciliation and compromising of political views that can stabilise civilian democracy and rule of law, both of which are essential to ... preventing extremism and violence from stalking the Pakistani people and the country", she said on Monday.
Sensitive to the perception that US pressure had forced the hand of Asif Ali Zardari, Pakistan's president, Clinton said the "Pakistanis themselves resolved the difficulties" without any US threat or demand.
But over the weekend, Clinton had called Zardari, who had repeatedly reneged on promises to restore Chaudhry, as well as Nawaz Sharif, leader of the opposition PML-N party.
General Rashid Qureshi, who served as an aide to Pervez Musharraf, the former Pakistan president, told Al Jazeera: "This decision was taken under pressure of the 'long march' ... The army chief could have said [to Zardari], please handle this politically.
"The whole of Pakistan is doubtful what this actually means. We should know in the next seven or eight days.
"I don't think [there is any] easy legal remedy for the complications Iftikhar Chaudhry has to resolve."
Sharif had thrown his weight behind Chaudhry and his followers had threatened to march on Islamabad, the federal capital.
Last month the supreme court ruled that Sharif and his brother, Shahbaz Sharif, were inelegible for elected office. Zardari then dismissed the government led by Shahbaz in Punjab, the most powerful Pakistani province.
Sharif recently told The Associated Press news agency that he would accept the court decision and leave the ruling Pakistan People's Party of Zardari to finish its term if it brought back Chaudhry.
The government now plans to appeal the court ruling disqualifying the Sharif brothers, a move welcomed by the PML-N.
Chaudhry will be under intense scrutiny when he returns to work on Saturday.
In Islamabad, hundreds of Pakistanis gathered on Monday outside the residence of Chaudhry, who stepped outside to greet and thank them.
Zardari's camp had painted Chaudhry as too politicised to return to such a critical post.
But many suspect Zardari also fears Chaudhry would allow legal challenges to a controversial pact signed by Musharraf that dismissed corruption cases against Zardari and Benazir Bhutto, the assassinated former prime minister.
That deal paved the couple's way back from exile and return to Pakistani politics.
Chaudhry's reinstatement has defused a potential violent confrontation between security forces and thousands of protesters as Sharif called off the opposition's "long march".
But fears remain over the country's security and the battle against the Taliban and al-Qaeda.
Police said late on Monday that a suicide bomber in a vehicle blew himself up outside a restaurant near a taxi stand in a crowded working-class area of Rawalpindi, which neighbours Islamabad.
"Fifteen people have been killed and 18 injured," Nasir Durrani, the Rawalpindi regional police commander, said on Tuesday, including the suicide bomber in the death toll.
Officials said the bomber was probably deployed to attack a mass protest, which had been scheduled in Rawalpindi and Islamabad on Monday, but was called off after the government's climbdown.
Also on Monday, fighters torched more than a dozen vehicles carrying supplies meant for US and Nato troops in Afghanistan, the second such assault in northwest Pakistan in two days.