Wrapping up her three-day official visit, Khar along with Foreign Secretary Salman Bashir and other members of the delegation spent over 30 minutes at the dargah in Nizamuddin in south Delhi.
Dressed in a salwar kameez, the 34-year-old Foreign Minister was accorded a traditional welcome by the office bearers of the dargah and was taken to Amir Khusro's grave where she offered a chadar.
Khar, who arrived here on Tuesday for talks with her counterpart S M Krishna, spent a few minutes there before proceeding to the shrine of Sufi saint Nizamuddin Auliya.
Since women are not allowed inside the shrine, she touched the chadar with her hand and gave it to other members of the delegation and office bearers who went inside and placed it.
Khar, the youngest Pakistani Foreign Minister, then offered prayers at the mosque adjoining the dargah where the priests asked her to pray for "peace between India and Pakistan."
"She prayed for peace between India and Pakistan and also for improvement of ties between the two countries. She was taken around the dargah by our nizamis and finally she also offered namaz," Diwan Syed Tahir Nizami, one of the office bearers of the dargah, told PTI.
He said they also prayed that Khar's purpose of the visit should be successful and "there should only be love" between the people of India and Pakistan. At the mosque, Khar offered namaz and was presented with a photograph of the Nizamuddin basti by the Dargah authorities.
Nizami said prayers were also held for Khar's "successful tenure" as Foreign Minister of Pakistan and for her future.
"Whoever comes to the dargah, they come with a prayer. They say their prayer in their mind. For Khar, we prayed for her successful tenure as Foreign Minister and also for her future," he said.
Media was not allowed inside the mosque and people jostled with each other to have a glimpse of Khar.