But Blackburn were aggrieved Ronaldo was still on the pitch after escaping a booking for a petulant kick at David Dunn.
As he went on to pick up a yellow card for a dive, the Rovers camp knew the world player of the year might have been sent off.
And irritation turned to fury later on as Rafael Da Silva put his hands on Morten Gamst Pedersen's shoulders inside the area, only for referee Howard Webb to rule there had been no foul as the Norwegian hit the ground.
"The boy Pedersen dived," argued Ferguson.
"There is no question about that at all. Yet Cristiano Ronaldo gets booked for the same thing and Pedersen doesn't.
"Both cases were the same. You have to give either a penalty or a yellow card."
Ferguson and Allardyce, who shared a post-match drink on Wednesday night, clearly reached a different conclusion.
"You would have to ask Howard Webb about the kick on Dunn. It was 56 minutes," said Allardyce.
"As far as Pedersen goes, Sir Alex has his opinion, I have a different one.
"Unfortunately, most clubs might not get a decision like that here. It wasn't a blatant one but it was a penalty. Pedersen got pulled and tugged."
It was the major talking point from a game United 'just about' deserved to win according to Ferguson, but one in which they also lost their magnificent defensive record.
After 1,334 minutes, United were finally breached by Roque Santa Cruz after a mix-up between Nani and Paul Scholes created an opening before Rio Ferdinand and Tomasz Kuszczak - standing in for the rested Edwin van der Sar - got involved in a tangle.
"It was a really bad goal to give away," said Ferguson.
"It was so soft and indicative of our performance really."
Wayne Rooney had put United in front when he finished off Nani's low cross that Ryan Nelsen had failed to cut out.
Then it was left to Ronaldo to profit from his reprieve by driving home a superb free-kick to put United eight points clear of Liverpool.
Ferguson's concerns are very different to those of Allardyce, whose team visit Coventry in an FA Cup fifth round replay on Tuesday still firmly entrenched in the relegation zone.
"We had a couple of opportunities to get ourselves in front, one just before half-time and another after it when Ryan Nelsen hit a post," said the Rovers chief.
"It would have been a real bonus for us today."