Cindy, 64, rested her head on the Stars and Stripes pall on what would have been her husband's 82nd birthday.
His body will lie in state before his final journey to the US Naval Academy in Washington DC.
John's daughter Meghan broke down in tears as his sons, Jack and Jimmy, saluted the casket.
His remains will be transported to DC on Friday where there will be a ceremony in his honour at the Capitol building.
A funeral will take place at Washington's National Cathedral on Saturday and he will be buried at Hospital Hill at Naval Academy Cemetery on Sunday.
Senator McCain's chopper pilot son Jack wore his white Navy uniform while brother Jimmy, a sergeant in the Arizona National Guard, wore his Army dress suit.
The Vietnam war veteran died on Saturday, aged 81, after a battle with brain cancer.
His coffin was led through a police parade and people on the street waved banners as it passed.
Republican governor Doug Ducey said in a speech: "Imagining Arizona without John McCain is like picturing Arizona without the Grand Canyon. It's just not natural."
As part of five day celebrations of his service to America, Senator MCcain will be honoured with a lone bagpiper
His adopted daughter Bridget and son from his first marriage, Andy, will give readings.
McCain slammed Donald Trump from beyond the grave after the President refused to pay tribute to the late senator.
In a posthumous statement, McCain took aim at Trump's policies – while the POTUS is said to have vetoed a White House statement hailing him a "hero".
Instead, Trump issued a curt 21-word tweet saying his “deepest sympathies” and prayers were with McCain’s family – before heading for a round of golf as the US mourned.
In McCain's statement, read out by close pal Rick Davis, the late senator hit out at Trump's plan for a wall on the Mexican border.
He blasted: "We weaken our greatness when we confuse our patriotism with tribal rivalries that have sown resentment and hatred and violence in all the corners of the globe.
"We weaken it when we hide behind walls, rather than tear them down, when we doubt the power of our ideals, rather than trust them to be the great force for change they have always been."
Flags which had been at half-mast over the White House were put back at full height yesterday.
But Trump soon backtracked AGAIN and returned the flag to half-mast “as a mark of respect”.
He also said that administration officials will attend the McCain memorials to “represent” him – confirming that he was not going.
Tributes to the veteran came from PM Theresa May, George W Bush and even Barack Obama, who beat McCain to the presidency in 2008.
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