Vogts, who was in charge of Scotland from 2002 to 2004, said he was made aware of a potential family link when Rooney was a highly-rated 16-year-old with Everton.
As it was Rooney made his England debut in February 2003, still aged just 17, and went on to become a star of the Barclays Premier League.
"I spoke to Wayne Rooney - his grandmother, she is Scottish," said Vogts, speaking in Baku ahead of his Azerbaijan side's World Cup qualifier against Northern Ireland.
"The Scottish Football Association found the grandmother and I made the call. I flew from Glasgow to Everton. He was playing under David Moyes at Everton and I spoke to him - a young lad of 16 years of age. I said to him 'you can play for Scotland'."
Explaining Rooney's reaction, the German coach beat his chest theatrically and said: "(Rooney told me) 'I am English, I am English!'. Okay, sorry.
"You have to speak to the player but he told me 'I'm so sorry boss, I'm English'."
For breaking stories and all the great banter like us on Facebook: facebook.com/tribalfootball