The Queen was able to celebrate her first Royal Ascot winner since 2008 courtesy of Estimate who landed the Queen's Vase in fine style under Ryan Moore.
The daughter of Monsun was the subject of solid market support beforehand and the 3-1 favourite went to the front two furlongs out.
She soon put the race to bed, storming clear under the former champion jockey to win by five lengths.
Athens (11-2) came through to claim the forecast spot with Ed De Gas (8-1) third.
Stoute said: "It's a great thing (to have a Royal Ascot winner for the Queen). We'd hoped to do it with Carlton House, but we've done it here.
"I think the whole country would have appreciated a victory for Her Majesty."
Of Estimate, Stoute added: "She's bred to stay. She's out of a real Aga Khan staying family with a Gold Cup winner in it and I felt after Salisbury she could be a Vase filly,.
"She's improved in her work of late and she's come and done it nicely. The Queen is delighted."
The Queen won the St Leger in Silver Jubilee year (1977) with Dunfermline, and Stoute was asked if Estimate might be aimed at the Doncaster Classic in September.
"I wouldn't have thought so at this stage. We will just have to see how she progresses," he said.
"It was great to come here with chances for Her Majesty. There was more pressure with Carlton House.
"We thought this filly might go well if she stayed, but I think if she had not been owned by The Queen she would have only been sixth favourite in the betting."
The Queen was fittingly presented with the winner's trophy by her husband, the Duke of Edinburgh.
Aidan O'Brien, trainer of runner-up Athens, said: "I was delighted with the run and we're delighted to be second to the Queen."