McDonald forced home an equaliser from close range in the fifth minute of injury time at Stark's Park to deny the First Division side a famous victory.
After the Dons' cup defeats to lower-league sides in the last four seasons - against Queen's Park, Queen of the South, Dunfermline and Dundee - McDonald saved their blushes in Kirkcaldy.
Raith had taken the initiative thanks to a superb 32nd-minute opener from Iain Williamson when the former Dunfermline midfielder scored sweetly on the volley from 20 yards.
John McGlynn's battling charges looked set to hold on in the face of growing Aberdeen pressure, but McDonald had the last laugh, netting after Sone Aluko's cross was knocked on by Charlie Mulgrew.
The 27-year-old celebrated in front of the 3300-strong away support after claiming a replay at Pittodrie on Tuesday week - and he felt Mark McGhee's men were worthy of at least a draw.
He said: "First half, I thought we played well but we just couldn't get that break until the end.
"We just wanted to keep going and going, we felt that goal was the least we deserved.
"I asked the referee (Willie Collum) at one point and he said there was five minutes left plus another five, so I knew there was a good wee bit of time to go.
"You don't think about our previous cup defeats on the park, obviously everybody else is going to point out things like that. We'll be confident of taking care of them up at Pittodrie."
Aberdeen's season looked in tatters until McDonald struck, keeping alive hopes of a place in the quarter-finals.
The Dons had their chances throughout but inspired goalkeeping from David McGurn, excellent defending from the likes of Mark Campbell and Grant Murray and poor finishing looked set to cost them.
But centre-half Zander Diamond's late entrance into attack ultimately helped break down Raith.
McGhee felt defeat would have been "an injustice" and wants his charges to use the goal as a turning point in their season.
McDonald added: "I knew if we just kept getting it in the box something might happen. Zander came on to help out and it has worked for us in the end thankfully.
"We have got Hibs away in the league on Wednesday night and we have to try and use that goal as a spur now."
Raith refused to point the finger at Collum for the additional time - given for a host of substitutions and an injury to Laurie Ellis - and instead simply licked their wounds.
Williamson added: "Gutted is the only word.
"I don't know about the injury time but they did have pressure and it was unfortunate they got the break.
"We're not out though. We didn't have any fear and they still have it all to lose."
Hibernian 4/5, Draw 5/2, Aberdeen 7/2
Source: Team Talk
Source: Team Talk