The young Villa side were under pressure for large portions of the first half, with Chelsea's Lewis Baker and Islam Feruz going close early on.
Villa grew into the game, with Jack Grealish and Callum Robinson causing problems out wide and they went close to taking the lead themselves when Graham Burke nearly scrambled the ball past Mitchell Beeney on 25 minutes.
After the break, Villa looked the more threatening side and were awarded a penalty on 49 minutes, when a clumsy piece of defending from Alex Davey brought down Callum Robinson.
Graham Burke coolly converted to give Villa a 1-0 lead.
Chelsea's Jeremie Boga looked to inject some pace into the game but Chelsea looked out of ideas and Villa appeared very comfortable off the ball.
Alex Kiwomya was sent off for the Blues as seconds ran out for the West London side and a second penalty from Burke in added time meant Villa were NextGen champions.
Chelsea's Lewis Baker was named player of the tournament after a run of superb displays that took the Blues to the final.