Baker suffered a sickening injury in the first half when he was struck in the face by a shot from Serge Gnabry.
He hit the ground and moved little before being carried away on a stretcher wearing an oxygen mask several minutes later.
It was later reported Baker had suffered mild concussion.
Lambert said: "He is a little bit groggy but he is okay. He can't remember a thing about what happened.
"That certainly threw us. You work all week on what you want to do and we lost him at a vital time."
It was not until the second half that they threatened again and Lambert thought their efforts might have deserved more.
He said: "That was more like it in the second half. I don't think if we'd got an equaliser anyone could have begrudged it.
"They responded fantastically and you could hear the crowd's reaction.
"The goal certainly gave us a huge lift to go again.
"We were playing against a top side with great ability - they are vying for the title and the Champions League - but we certainly gave them a fight."
Christian Benteke again looked ineffective until putting Villa back into contention with a back-post header.
He then looked a different player and Lambert hopes there is more to come.
He said: "About this time last year he started to hit the goals. It is quite uncanny. It will certainly give him a big lift."
Lambert played down rumours linking Villa with a loan move for Wigan striker Grant Holt.
He said: "Holty was fantastic for me at Norwich. He is a proper guy. I have just heard the rumours are everywhere but until something is concrete then I won't say."
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