The actress, who was here for a week to shoot for Priyadarshan's film "Bhool Bhulaiya", Sunday visited the dargah, 130 km from Jaipur.
The comic thriller, a remake of Malayalam super-hit "Manichitrathazu", also stars Akshay Kumar, Vidya Balan and Paresh Rawal.
"Amisha spent nearly 10 minutes in the dargah after arriving at 11.30 a.m. by an auto-rickshaw," a dargah committee member told on phone from Ajmer.
The actress was dressed in a black burqa to avoid members of the media and her fans and was accompanied by security personnel, he added.
Owing to Chati - a Muslim ritual - the dargah was full of devotees offering chadars to the saint.
"Amisha offered the chadar and flowers and tied wish threads. After offering prayers, she sat on Khadim Zahoor Baba's gaddi (seat) in the dargah before leaving for his residence in Ratidang," the committee member added.
The shrine, dedicated to the Sufi saint who came to Ajmer from Persia in 1192, attracts thousands of pilgrims during Urs, an occasion commemorating Chisti's death anniversary.