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.
For all Reading's early promise they almost fell behind after 12 minutes when Benteke rattled the crossbar with a header.
Reading's opener after 31 minutes, however, will be consigned to the blooper reel as Baker was left red-faced by his bumbling generosity.
There appeared little danger, despite Hope Akpan helping Jobi McAnuff's low cross on, but defending close to his line Baker horribly rushed his clearance and watched on as it bounced off his standing leg and over the line.
Reading's lead lasted barely two minutes, though, as Benteke lashed in a shot that took a deflection off Stephen Kelly to ensure third-choice goalkeeper Stuart Taylor was beaten.
It got worse for the Royals as they conceded in first-half injury time for the second successive game at home.
Following a patient build-up by Villa, Matthew Lowton headed the ball across the six-yard box and while Barry Bannan's deft touch rebounded off the post Taylor could only help the loose ball on to Agbonlahor to thump home.
Reading thought they were level 10 minutes after the re-start only for a marginal offside call to go against them. Noel Hunt poked home at close range but if he was not offside Adam Le Fondre, who was just in front of him, appeared to have just strayed. The home side kept pushing but there was no late rally on this occasion.