Mr Austin and Mr Shoigu discussed the importance of keeping the lines of communication open between Washington and Moscow amid Russian President Vladimir Putin's war against Ukraine, the Pentagon said in a readout of the call.
The Pentagon in March said it had established a hotline with Russia's defence ministry to prevent “miscalculation, military incidents and escalation”.
The US has created hotlines to stay in communication with Russia during previous moments of tension, including after Moscow intervened in the war in Syria to back President Bashar Al Assad.
In a separate call on Friday, Mr Austin spoke to Ukrainian Defence Minister Oleksii Reznikov to “reiterate the unwavering US commitment to supporting Ukraine's ability to counter Russia's aggression”, the Pentagon said.
Mr Austin highlighted the international community's continuing support of Kyiv's defence capabilities, pointing to the commitments the US and its partners made at the Ukraine Defence Contact Group meeting earlier this month.
Both Mr Austin and Mr Reznikov pledged to remain in close contact, the Pentagon said.
Since Russia invaded Ukraine on February 24, the US has committed more than $16.8 billion in military aid to Kyiv, including Himars, Javelins, armoured vehicles and other defence equipment.