Mark Hughes' Potters strolled to their first away win in seven months thanks to a woeful defensive display from Villa.
Christian Benteke gave Villa an early lead after smashing home a left-footed strike, but Stoke dominated thereafter.
Peter Odemwingie scored his third goal in two games to equalise and four minutes later Peter Crouch took advantage of slack marking to put Stoke ahead with a sidefooted finish.
Leandro Bacuna and Nathan Baker both failed to clear their lines and Steven Nzonzi took full advantage, beating Brad Guzan from inside the box.
Geoff Cameron rounded off the hammering in the final minute as Villa's defence was stretched on the counter.
Lambert was disappointed his "second best" side lost their lead, and would not make excuses for them.
Villa lost Karim El Ahmadi and Andreas Weimann to injury within a minute of each other in the first half, but Lambert said on Sky Sports 1HD: "We were definitely second best. That wasn't good enough.
"We got off to a really good start, within five minutes things were looking okay - we lost a couple of lads to injury, Andy and Karim - but (beside that) we were still second best.
"Andy had a severe dead leg that he couldn't shake off. We will have to see how he is. Karim has a little thigh strain.
"We had a really good start and got a really good goal, but the goals we lost were really, really poor.
"We take nothing away from Stoke, they deserved to win the game.
"(The injuries) do disrupt you a little bit but I'm not going to use that as an excuse."
Next up for Villa is a trip to Manchester United next weekend and Lambert is confident his side can put in a good display following last week's 1-0 victory over league leaders Chelsea.
He added: "We'll be really up for it. Like the Chelsea game, no one expects us to get anything.
"It's a great game to play. As a footballer you want to play these sort of games and it's up to us to try to get something from them."
The poor performance came as a shock to Lambert after successive home wins over Norwich and Chelsea, and he added: "The whole performance was unlike us. We looked lethargic.
"We never got going and you try and get a goal back and it just never materialised."