Several people have been injured in clashes
At least a dozen people were injured in the clashes close to the Shahbaz airbase, which several militant Islamic groups claim is being used as a launch pad for the campaign against neighbouring Afghanistan.
The protesters had managed to evade the tight security that has been set up in and around the city ahead of a planned rally at the airbase, called by the country's largest Islamic party - Jamaat-e-Islami.
The head of Jamaat-e-Islami had also been prevented from travelling to Jacobabad.
Heavily armed officers have been patrolling the streets of the city and more than 100 people were arrested in the morning after they attempted to stage a small protest in the city centre.
Pakistani President Pervez Musharraf has come down hard on those opposed to his co-operation with the US, although he has now made clear he wants the US campaign over before Ramadan begins next month.
Islamic leaders around the world have expressed concern that if the US strikes continue into this Muslim holy festival, which starts in mid-November, there could be major unrest.
Planned siege
The authorities have been keen to prevent a repetition of anti-American demonstrations like one earlier this month in Jacobabad, when one man died after police opened fire on an angry crowd.
At least 3,000 security officers have been drafted into the area, and trees and trucks have been used to block roads in order to stop people entering the city.
The protesters have threatened to lay siege to the base, which the US and Pakistan insist is being used only for US search-and-rescue missions - not to launch attacks.
Police had started to make arrests in the run-up to the rally. Jamaat-e-Islami said that over 1,000 supporters had been taken into custody by Monday night, although the authorities said the figure was considerably lower.
Qazi Hussain Ahmed, leader of Jamaat-e-Islami, was handed a travel ban when he arrived at Lahore airport for a flight to Jacobabad on Monday.
The party leader said he would challenge the travel ban in court, and issued General Musharraf with a warning.
"The days of this government are numbered, and Musharraf will no longer be in power after a few days," Mr Ahmed said.