Shotton was given his marching orders by referee Roger East for a second bookable offence but replays showed he made no contact on Villa substitute Fabian Delph. Villa striker Darren Bent made his return to action as the home side's youngsters stood up to the physical challenge presented by Stoke.
Bent made his first appearance for nearly six weeks midway through the second period but was unable to inspire Villa to gain the three points. Paul Lambert's side were well worthy of a share of the spoils, though, as they extended their unbeaten run to four games and edged further away from the relegation zone.
Villa's 'tiny tots' looked ready-made for Stoke to impose their physical presence on them but they passed the challenge with flying colours. Stoke will also take heart from extending their unbeaten run to six games, from which they have collected 14 points, and they have now registered eight clean sheets this season.
The Potters were indebted to a crucial block from skipper Ryan Shawcross to keep out Christian Benteke's close-range volley after Ciaran Clark had headed the ball back across goal. Matthew Lowton then had the confidence to cut inside and create space for himself but his left-footed drive did not extend Stoke goalkeeper Asmir Begovic.
Barry Bannan then curled a free-kick over the bar after Benteke had been brought down by Geoff Cameron 20 yards out. Stoke midfielder Steven N'Zonzi appeared to flick a hand in the face of Villa centre-back Nathan Baker in the build-up to a Potters corner but both players were spoken to by referee East.
Stoke were incensed by a centre-circle challenge on Glenn Whelan by Clark in first-half stoppage time but it escaped any punishment. Villa started the second half brightly and Begovic went down to his left to cling onto Benteke's volley after Lowton had flicked on a Bannan cross.
Benteke continued to ask questions of Stoke and some trickery inside the area created half a chance but Robert Huth reacted quickly to block his shot on the turn.
Lambert brought on Bent and Stephen Ireland for Gabriel Agbonlahor and Brett Holman midway through the second half while Stoke replaced Matthew Etherington and Kenwyne Jones with Cameron Jerome and Peter Crouch.
Shotton became the first player to be yellow-carded after 75 minutes after fouling Ireland. Then came his stoppage-time red card, although there was no time left for Villa to cash in on their numerical advantage.
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