Thirty priests performed the puja in the presence of office bearers of the shrine management committee, representatives of the Shankaracharya, officials and local legislator Shaila Rani Rawat.
Chief Minister Vijay Bahuguna was scheduled to take part in the puja but inclement weather forced him to abort his travel plans to Kedarnath. Guptakashi and Kedarnath areas were hit by rains Wednesday morning.
The temple was decorated with flowers, and the nearby platform and other places which were damaged in the June floods, were covered with marquees.
The priests first performed "shuddhikaran" (cleansing) puja, after which the deity at the sanctum sanctorum was bathed in milk, holy water from the Ganga river, and other items were used in the puja of Lord Shiva, state government officials said.
Hundreds of people died in the floods in Uttarakhand in June. Over 160 bodies were found near Kedarnath last week alone.
The date for opening the temple was fixed in August at a meeting between government officials and the temple management.
Officials, however, said it would take some time before the temple is opened to the public. This was because the approach roads to the temple are in bad shape and would take a long time to rebuild, an official told IANS.
The temple premises were cleared of debris and the bodies over the last two months.