The News International chief executive was asked at the Leveson Inquiry on Wednesday whether he had accepted four places offered by the First Minister to see the show at St Ann's Warehouse in Brooklyn in 2007.
Murdoch responded by saying "I'm afraid not" when asked by QC Robert Jay if he had attended.
But last night, it emerged the theatre company, which is funded by the Scottish Government, said it was their "understanding" the tycoon was in the audience of the hugely successful play about the Scottish regiment in Iraq.
It said in a statement: "The National Theatre of Scotland was asked by the Scottish Government in late autumn 2007 to make available four tickets for Rupert Murdoch to attend a performance of the company's production of Black Watch during its run at St Ann's Warehouse in Brooklyn, New York. These tickets were provided for a performance on 3rd November, 2007.
"It is the National Theatre of Scotland's understanding that Mr Murdoch did attend."
At the inquiry, Mr Murdoch was questioned about a letter sent to him by Mr Salmond on 31 October, 2007.
"He writes to you again on 31 October - inviting you to go to see a play called 'Black Watch' in New York, but warning you that it's quite challenging: 'A rough, tough production.' Did you go and see that play?" Mr Murdoch said: "I'm afraid not."