Defender 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 readymade for Stoke to impose their physical presence on them, but they passed the challenge with flying colours.
Stoke will 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.
Shotton was yellow-carded after 75 minutes for a foul on Ireland, and then came his red card, although there was no time left for Villa to cash in.