Toner, 20, has put pen to paper on a deal that will keep him at the Northern Commercials Stadium until the end of the current 2016/2017 campaign.
The Irish centre half enjoyed a successful spell on loan at fellow Sky Bet League One side Walsall during the first half of the season, starting twenty times in all competitions for the Saddlers.
Hailing from Ashbourne, County Meath, Toner has been capped at Under-19 level for the Republic of Ireland.
The promising defender also featured four times for Aston Villa's first team last season towards the end of their Premier League campaign.
After making his Premiership debut at home to Southampton as a half time sub last April, Toner started Villa's subsequent games against Watford, Newcastle United and Arsenal.