The inspirational 36-year-old laid on both goals in the second half to finally reward his team's all-round supremacy against limited opponents.
Stoke strung five players across midfield in an attempt to suffocate United's creativity, leaving Dave Kitson to battle away on his own up front.
Predictably, it was all United early on with Wayne Rooney and Paul Scholes striking volleys before Antonio Valencia squandered a great chance to open the scoring in the eighth minute.
The winger only had Thomas Sorensen to beat after skipping beyond Ryan Shawcross, but dragged his chip a foot wide of the keeper's right-hand post.
It was so one-sided Stoke could have done with another ball as United attempted to pick more holes in the home team's massed ranks.
Sorensen saved at full stretch from Nani and Shawcross blocked a pile-driver from Dimitar Berbatov as Stoke withstood the onslaught until half-time.
Former Stoke goalkeeper Ben Foster hardly touched the ball in the first half, but the home side thankfully decided to be more adventurous after the break.
A couple of long throws from Rory Delap and a chip by Liam Lawrence, easily clutched by Foster, finally gave an unusually subdued home crowd something to chew on.
And with United's attacks much less frequent, Ferguson brought on his talisman Giggs for Nani in the 56th minute.
And Giggs had only been on the field for six minutes when he collected Darren Fletcher's pass and slid a perfect low cross for Berbatov to roll in easily from four yards.
Stoke now had to chase the game and Tony Pulis introduced James Beattie and Tuncay for a tiring Kitson and midfielder Dean Whitehead.
But it was all over 14 minutes from time with Giggs providing his second assist. He bent a free-kick from the right straight onto the head of John O'Shea and the big defender's glancing effort flew into the top right-hand corner of Sorensen's net.