Daniel, who has been the Metropolitan of the northeastern regions of Moldova and Bucovina for the past 17 years, was chosen as the country's sixth Patriarch, after a 40-day mourning period for his predecessor Teoctist, who died in July.
"I want to serve the church as Teoctist did," Daniel told reporters after the election, which he won by 95 votes out of 161.
In 1999, Teoctist invited the late Pope John Paul to Romania, the first time a Catholic Pope had visited a mainly Orthodox country in a trip aimed at narrowing the age-old split between the two churches.
Religious observers say Daniel is a leader of the reformist arm of the Romanian Orthodox Church, promoting good relations with other Christian churches.
During the 40 days of mourning for Teoctist, local media accused western-educated Daniel of collaborating with the feared Securitate, the secret police during communist rule. He has not commented on the charges.
The National Council for Studying Securitate Archives confirmed it was investigating top clerics, but declined to offer any names.
Some observers say one of his main tasks as Patriarch would be to continue Teoctist's project to build a "Cathedral of the Nation's Absolution".
Like the Christ the Saviour cathedral in Moscow, it was to be regarded as a symbol of rebirth after 50 years of communist repression, but land and financing problems have delayed construction.