The call, which was initiated by Moscow, comes as tensions between the two sides flare over Washington's plan to deploy long-range missiles in Germany, a decision the Kremlin warned could spell a return to Cold War-style confrontation.
"The issue of preventing security threats and reducing the risk of possible escalation was discussed," Russia's defence ministry said in a statement on the talks.
According to Deputy Pentagon Press Secretary Sabrina Singh, Austin "emphasized the importance of maintaining lines of communication" during the conversation.
The two sides have managed to organise sporadic phone calls despite raging tensions over the conflict in Ukraine, including a recent call at the end of June where Moscow chided Washington's arms supplies to Kyiv.
The White House announced on Wednesday during a NATO summit that it would station long-range weapons including Tomahawk cruise missiles in Germany as a deterrent.
The Kremlin criticised the move, accusing Washington of taking a step towards a new "Cold War" and of directly participating in the conflict in Ukraine.
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