Fifteen people aboard the Russian reconnaissance jet died when the Syrians shot it down, responding to an Israeli missile strike.
Russian Defense Minister Sergei Shoigu told his Israeli counterpart, Avigdor Lieberman, that Israel "bears full responsibility" and that Russia had the right to retaliate.
But Putin stepped in, calling it "a chain of tragic, accidental circumstances." He said Russia would respond by "taking additional steps to protect our servicemen and assets in Syria." He said "everyone will notice" those steps.
Israeli Prime Minister Benjamin Netanyahu expressed his sorrow at the loss of Russian lives and blamed Syria for the incident.
The Israeli military said its jets were targeting a Syrian military facility supplying arms to the Iranian-backed terror group Hezbollah.
Israel said it had warned Russia of the airstrike in advance, and its jets were already back in Israeli airspace when Syria fired its missile.
The Russian defense ministry said Israel's warning came less than a minute before the airstrike. It accused the Israelis of using the Russian plane as a cover to avoid Syrian air defense systems.
While Putin did not appear to blame Israel outright for causing the Russian plane to be shot down, the Kremlin said it told Netanyahu that Israel had violated Syrian sovereignty and urged it "not to let such situations happen again."
President Donald Trump told reporters at the White House that, based on what he had been told, Syria shot down the Russian plane. He called the deaths of those aboard "a very sad thing."
Trump took a moment to say the United States has done a "tremendous job" in helping eradicate Islamic State from Syria and said "we are very close to finishing that job."
Putin is striving to maintain his good relationship with Israel, while continuing to back the Syrian government in its fight against the rebels.
Russia also has healthy relations with Iran, Israel's archenemy.
Israel has said it will not allow any permanent Iranian military presence inside Syria and has looked to the Russians to help keep Iranian-backed forces away from the Israeli-Syrian frontier.