Under the law of special investigations, his first deputy Saulius Urbanavičius will work as acting director on a temporary basis, the President's Office said in a press release.
At his own request, Pacevičius was dismissed after expiry of his term in office. The decree is effective from the day of signing.
On Tuesday, the Lithuanian parliament backed Grybauskaitė's decree and dismissed Pacevičius in a second ballot.
Pacevičius served as Lithuania's SIS chief from October 2007. His five-year term ends on 17 October.