Challenging the Centre's decision, the CPI(M) said in its petition that the move undermined democracy and it would lead to greater political corruption.
Yechury said the party was left with no choice but to move the apex court.
He said they had taken up the matter in Parliament and sought amendments to the bill when the government moved the proposal.
"Using their majority in Lok Sabha, the government overturned the Rajya Sabha's recommendations. The no disclosure clause in electoral bonds will create opacity in funding and is bad for democracy," he claimed.
The move was resisted by opposition parties. The Election Commission also expressed its reservations initially.
It is rare for a political party to approach the Supreme Court in such matters.