Triple world champion Stewart had fallen out badly with Senna when he accused him of deliberately running arch-rival Prost off the track for the 1990 title.
"I am never going to speak to you again," Senna had told Stewart, according to the Scot in an article for the Daily Mail newspaper last week, marking the 20th anniversary of his death at Imola.
Stewart claims he made up with Senna a year later, and also the bitter acrimony between Senna and Prost had also eased by 1994, following the Frenchman's retirement.
Nonetheless, Assumpcao revealed her horror when she arrived for the funeral to discover that Stewart and Prost would be at the very front of the casket.
She said her arrival was delayed after helping friends, family and international guests to make their way from the city to the Morumbi cemetery.
"Gerhard Berger, Ayrton's best friend in F1, ran to me and cried 'Betise, you must do something'," Assumpcao recalled.
"Someone told me that Alain and Jackie will be at the front of the coffin -- apparently it's in order of world titles!" she added, recalling Berger's words.
"You have to change it," Berger told Assumpcao. "They are the two people Ayrton hated the most in his life'.
"He (Berger) was horrified and frankly, so was I. My stomach started to hurt.
"I turned quickly and went to the cemetery gate. On the way, I bumped into Geraldo Rodrigues, Rubens (Barrichello's) manager and a dear friend.
"I told him 'You won't believe it. They want to put Jackie Stewart and Alain Prost right at the front. Ayrton will be turning in his coffin!" she said.
"There was no doubt in my mind that Gerhard had to be right at the front," added Assumpcao. "He had been with Ayrton in most of the good times with Ayrton, on and off the track."
She put another Brazilian world champion, Emerson Fittipaldi, alongside him.
In the end, Prost pushed the coffin trolley in the position behind Fittipaldi, with Stewart a further two places behind.
"I went back to where the drivers were and pretended I didn't know anything of the previous arrangements.
"I think Ayrton would have been happy to see me, helping his friends and making decisions without hesitation. He was like that," Assumpcao added.