Police stopped a convoy of 75 vehicles, carrying over 250 persons including women, on Andhra Pradesh-Tamil Nadu border near Sullurpet in the district.
The protesters, carrying placards and flags, shouted slogans against Rajapaksa before heading back to Tamil Nadu, said Deputy Superintendent of Police B Srinivas.
Andhra police have tightened security in the border areas. The roads leading Tirupati from Tamil Nadu have been closed.
"A full-fledged security arrangement has been made. Rajapaksa is scheduled to fly back to Sri Lanka tomorrow after offering prayers to Lord Balaji," Deputy Superintendent of Police Ravishankar Reddy told PTI.