The Golden Temple was damaged in 1984 during an army raid ordered by then Prime Minister Indira Gandhi to flush out Sikh militants fighting for an independent state.
The rebels, led by Sant Jarnail Singh Bhinderanwale, had turned the temple into their stronghold, massing arms and ammunition there. Bhinderanwale was killed in the army assault.
Santa Singh was punished for defying an edict by the Akal Takht, the top Sikh temporal authority, to boycott the repair ordered by the government.
Last month, Singh apologized to Joginder Singh Vedanti, head of the Akal Takht, and sought forgiveness for his act.
Vedanti suggested penance, including a weeklong prayer, and fined him 1,101 rupees (dlrs 23.40).
On Wednesday, Singh was welcomed back to the Akal Takht by Sikh priests.
Nearly 2,000 supporters of Singh, in traditional blue clothes and turbans, thanked the Akal Takht chief for his forgiveness.
``I realized that without the Akal Takht and by opposing the verdict of the Akal Takht, a Sikh cannot become a real Sikh. I am very happy today because the Sikh clergy has accepted my appeal for forgiveness,'' Singh said.
The military assault on the Golden Temple in 1984 had outraged the Sikh community and led to the assassination of Prime Minister Gandhi by her Sikh security guards.
The militancy in northern Punjab state was wiped out by the government in 1994.