Party for Freedom (PVV) leader Geert Wilders had proposed the vote of no confidence against Rutte for his reaction on Zijlstra's lie, and he was supported by five other opposition parties.
The motion didn't get a majority vote.
Earlier on Tuesday, Zijlstra announced his resignation just before a debate on his position in the Dutch lower house of parliament.
The pressure on him was too high after the 49-year-old FM had admitted in Dutch newspaper de Volkskrant on Monday that he lied on having being present at a meeting with Putin in 2006. One day later he also appeared to have misinterpreted words of Putin on a "Great Russia".
The debate continued without Zijlstra, but with Rutte, who had to defend his decision to initially support Zijlstra and why he did not inform the parliament immediately after he heard about Zijlstra's lie on Jan. 29.
Rutte admitted he made a mistake and he blamed himself for underestimating the seriousness of the case when Zijlstra informed him two weeks ago about the forthcoming article in de Volkskrant.
"I thought he could continue as a minister with a good explanation," said Rutte. "I found his lie a sin, but not a mortal sin."
Sigrid Kaag, Minister for Foreign Trade and Development Cooperation, will temporarily take over the tasks of Zijlstra as FM until a successor is found.