In the end, a toothless display from the Potteries outfit meant United were able to cruise home 2-0 winners thanks to penalties either side of the interval from Javier Hernandez and Dimitar Berbatov.
However, it looks as though United will be forced to rely on 21-year-old third-choice keeper Ben Amos at Chelsea on Sunday, which is hardly an ideal scenario and Ferguson said: "Anders (Lindegaard) got injured in training and David (De Gea) got injured at the end of training, so we had a right nightmare."
He added: "Ben didn't have a lot to do but he was confident and composed, so we are pleased with that."
Stoke boss Tony Pulis admitted he wanted to work Amos more on his Premier League debut.
However, the Macclesfield-born keeper only had one shot of note to save, from substitute Cameron Jerome, as United profited from fouls by Jermaine Pennant and Jon Walters on Park Ji-sung and Antonio Valencia either side of the interval.
"The first one was very debatable," said Pulis. "The second one was [a penalty]... and the one he didn't give - for a foul on Patrice Evra - was a definite penalty."
TV replays suggested referee Mike Jones got it right with the first decision. There was little debate over the quality of Hernandez's finish and Berbatov was equally emphatic when he assumed responsibility for the second spot-kick.
"It was a very good penalty," said Ferguson of Hernandez's effort. "But he takes them for Mexico so it wasn't a problem. Dimitar thought he was going to take the first one so he took the second one and he scored too so we're pleased with that. It has been a good night."
The result, coupled with Manchester City's surprise defeat at Everton, means United are now level on points with their local rivals, whom they trail on goal difference.
Source: PA
Source: PA