His closest aide, Finance Minister Tendai Biti, said: "We're so traumatised, brutalised, we couldn't feel the pain. Why, why, why?"
Suspicions have swirled over Mrs Tsvangirai's death given past acrimony between the prime minister and president, although Mr Tsvangirai said on Monday it was unlikely foul play was involved.
In his first public comments on the crash, Mr Mugabe told Tuesday's church service: "I plead with you to accept it, it's the hand of God."
Mr Mugabe continued: "We are sincerely saddened by the death of Susan and we hope that Morgan will remain strong."
The 85-year-old leader, whose supporters were accused of launching deadly attacks on opposition activists during last year's elections, added that the environment in the country should not be conducive to violence.
'Life goes on'
The body of Mrs Tsvangirai rested in a flower-draped coffin during the service, attended by her husband and children.
Most of the new administration which shares power between Mr Mugabe's Zanu-PF and Mr Tsvangirai's Movement for Democratic Change (MDC) were also present at the Methodist church.
Mrs Tsvangirai, who kept largely away from the political limelight, is to be buried on Wednesday near the couple's rural home in Buhera, Manicaland Province.
Many mourners have already visited the Tsvangirai family home
The driver of the truck that hit the couple's car has been charged with culpable homicide.
Chinoona Mwanda, 35, who was bailed on Monday, is to plead not guilty, blaming the collision on the poor state of the road, his lawyer said.
In spite of his bereavement, Mr Tsvangirai said on Monday "life had to go on".
The Tsvangirais, who had been married for 31 years, were travelling to Buhera when the crash occurred near Beatrice on Friday afternoon.
Mr Mugabe and his wife Grace visited Mr Tsvangirai's bedside hours after the crash as he was treated for minor injuries at a private clinic in the capital.
The British foreign ministry has said the truck in the crash was part of an aid project and it appeared to be "a genuine accident".
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