Hundreds of supporters had gathered around him as protest organisers played Buddhist prayers over a public address system.
The supporters dispersed after Weerawansa was taken away in an ambulance.
Ban asked Sri Lanka on Friday to "normalise conditions" around the UN office in Colombo after days of angry demonstrations. Earlier in the week he recalled the UN's top envoy to the island, Neil Buhne, for consultations.
The UN chief's office said the "strong reaction" to the UN probe was "not warranted," adding the expert panel was acting only in an advisory role.
The UN has previously reported that at least 7,000 ethnic Tamil civilians were killed in the final months of fighting last year.
Foreign Minister Gamini Lakshman Peiris told parliament Ban acted too hastily in summoning his top envoy back to New York and by closing a UN office near the protest site that served 34 countries in the region. Legislator Wimal Weerawansa ended what he had called his "death fast" after President Mahinda R