The Royals were gifted the lead on the half-hour when Baker made a complete hash of a routine clearance but on a day when neither defence was convincing it was not decisive.
Instead, Villa were level two minutes later when Christian Benteke fired in before Gabby Agbonlahor grabbed the winner in first-half injury time.
Victory was just Villa's second in their past 12 league games and moved them three points clear of danger.
Reading's defeat - their second in succession at home against a relegation rival after they lost 3-0 to Wigan a fortnight ago - left them above last-placed QPR on goals scored only.
Lambert said: "I though Nathan Baker was exceptional. He has been for the past number of weeks since I've put him at left-back.
"It was important his head never went down which it didn't. Being young the slight thing in my head was how he reacted. I've got to give him so much credit."
Agbonlahor's strike capped a patient Villa move, which did require some poor Reading defending as well, as Stuart Taylor could only scoop Barry Bannan's deft touch against the post into the forward's path.
"I thought the goal was brilliant," Lambert added. "I think there was 20-odd passes and the finish was world-class. Some of our football was excellent. It was a massive game."