Burnley often matched Villa for long spells and the Clarets went down as a result of Kevin Phillips third goal of the season.
The win left more questions than answers about Villa's immediate prospects and the failure of their most expensive signing, Juan Pablo Angel, to open his goalscoring account for the season is proving a major problem.
The one bonus from this game was the successful return of Welsh international defender Mark Delaney who began his first game of the season for Villa. He made an immediate impact and could not have timed his return better for struggling Villa.
Burnley, making their first visit to Villa Park in 30 years, competed well and never lost heart with Ade Akinbiyi often setting a fine example.
Villa, beaten 3-1 by Burnley in the same round last season, made some determined early raids in a bid to make amends for the defeat at Turf Moor. But Burnley are noted for their defensive play away from home and battled gamely in the early stages.
The most dangerous moment for Burnley occurred in the first minute when Stephen Davis just failed to make contact with his head following a left-wing cross from Gareth Barry.
Akinbiyi, playing as Burnley's lone front man, managed to upset both Olof Mellberg and Liam Ridgewell with his robust play but he lacked support to really test Villa's goalkeeper Thomas Sorensen.
Villa, 8-3 winners at Wycombe in the previous round, were keen to make amends for their 2-0 home reverse at the hands of Wigan last Saturday and they maintained a strong tempo for the first 15 minutes
A compact Burnley survived the early onslaughts with Gavin McCann often the driving force in mid-field for Villa but in the 22nd minute the Clarets had to surrender when Phillips finally broke the stalemate.
Angel won possession and rolled the ball to Phillips who moved forward to play a quick one-two with James Milner before slotting a low shot past Brian Jensen.
The expected goal avalanche failed to materialise as Villa's shortcomings in attack persisted as they struggled to overcome mediocre opposition.
Their failure to build up an emphatic advantage only emphasised the general failings and next Monday's trip to Manchester City can hardly be viewed with a great deal of confidence.
Burnley resolutely kept at their task. Skipper Frank Sinclair kept a tight ship at the back, while Chris McCann always made sure Villa where unable to rest on their laurels.
The result was that Villa became extremely edgy in the closing stages when Wade Elliott and James O'Connor caught the eye.
A dejected Angel departed from the scene in the 78th minute and his replacement, Luke Moore, forced Jenson to make his best save of the game in the closing stages when Burnley could easily have equalised.
Substitute Gifton Noel-Williams had a glorious chance but saw his effort deflected away for a corner as Villa made hard work of their belated win.