Speaker Manohar Joshi said the vote was 312 to 186 against a no confidence vote.
Congress Party leader Sonia Gandhi, who called for the vote, told the BBC the motion was born out of concern for the direction the country is taking. She said her party intends to force the government to address what the opposition calls corrupt arms deals.
Vajpayee had questioned the vote: "I can't understand what is the pressing concern now. There is no question of breaking up the government because it won't happen. Perhaps, the grapes are sour for the opposition."
Indian newspapers called the debate a "curtain raiser" to key state elections scheduled later this year.