Thirty priests performed the puja in the presence of office bearers of the shrine management committee, and representatives of the Shankaracharya.
The temple was decorated with flowers, and the nearby platform and other places that were damaged in the June floods, were covered with marquees.
The priests first performed the shuddhikaran (cleansing) puja, after which the deity at the sanctum sanctorum was bathed in milk, holy water from the Ganga river, and other items used in the puja of Lord Shiva.
The date for opening the temple was fixed in August at a meeting between government officials and the temple management.
Officials, however, had said it would take some time before the temple was opened to the public.
The temple premises were cleared of debris and bodies over the last two months.