Yoan Gouffran netted the opener from four yards and another goalmouth scramble resulted in Henri Lansbury turning the ball into his own net.
But Newcastle's victory was soured by the loss of top scorer Dwight Gayle, who limped off after 33 minutes.
Villa striker Scott Hogan was carried off on a stretcher late on and they are now winless in nine league matches.
Hogan, who cost £12m from Brentford in January, landed awkwardly after challenging for a header at a late Villa corner.
Gayle - the Championship's leading scorer with 20 league goals this season - appeared to suffer a recurrence of the hamstring problem which had kept him out for six matches.
Villa remain six points above the relegation zone, having collected only one point in 2017, although Steve Bruce's side had more than matched the Magpies until they fell behind.
Iceland midfielder Birkir Bjarnason went closest for the visitors, failing to hook in Hogan's flick-on from close range and later having a shot saved by Karl Darlow.
Newcastle's opening goal came soon after Gayle's departure, with Villa failing to properly clear a Matt Ritchie cross and French winger Gouffran tapping in.
After that, the hosts took control and often looked likely to extend their lead, although the second goal which took them above Brighton in the table came in fortunate circumstances.
Jamaal Lascelles met Jonjo Shelvey's corner and his effort hit Lansbury, who was stationed at the near post, before ricocheting into the net.
Newcastle manager Rafael Benitez told BBC Radio Newcastle: "This is a very difficult division. Every game is tough and we were playing against a good team with very good players.
"They pressed well at the beginning and it wasn't easy for us to play how we wanted. We needed to score to open up the game, and after the second goal it was more open. We had more chances and more control of the game.
"Dwight Gayle seemed like he wasn't comfortable from the beginning and then he said he was feeling something in his hamstring. We don't know how serious it is. We have to wait."
Aston Villa manager Steve Bruce told BBC WM: "Scott's injury compounded the night, because we obviously fear the worst.
"He's definitely turned his ankle over and we don't know how serious it is until we see X-rays and scans. The consequences of losing him are huge, but let's hope it's not as bad as what we think.
"I thought we were decent in the first half, Newcastle hadn't been near our goal, and yet we gave a poor goal away. After the restart, we've given another one away and the second one was comical.
"And the two or three opportunities we've had, we've not taken them. That's where we are at the moment."
Substitution, Newcastle United. Christian Atsu replaces Yoan Gouffran.
Delay in match Scott Hogan (Aston Villa) because of an injury.
Corner,  Aston Villa. Conceded by Matt Ritchie.
Foul by Yoan Gouffran (Newcastle United).
Gary Gardner (Aston Villa) wins a free kick in the defensive half.
Substitution, Aston Villa. Leandro Bacuna replaces Jonathan Kodjia.
Delay over. They are ready to continue.
Substitution, Aston Villa. Gary Gardner replaces Birkir Bjarnason.
Delay in match Jonathan Kodjia (Aston Villa) because of an injury.
Attempt missed. Jonjo Shelvey (Newcastle United) right footed shot from more than 40 yards on the right wing is high and wide to the right from a direct free kick.
Mohamed Diamé (Newcastle United) wins a free kick on the right wing.
Foul by Neil Taylor (Aston Villa).
Attempt missed. Jonathan Kodjia (Aston Villa) right footed shot from the left side of the box is high and wide to the left. Assisted by Albert Adomah with a cross.
Matt Ritchie (Newcastle United) wins a free kick on the right wing.
Foul by Neil Taylor (Aston Villa).
Substitution, Aston Villa. Albert Adomah replaces Mile Jedinak.
Attempt saved. Jack Colback (Newcastle United) left footed shot from the left side of the box is saved in the bottom right corner. Assisted by Aleksandar Mitrovic.
Attempt saved. Aleksandar Mitrovic (Newcastle United) header from the centre of the box is saved in the top centre of the goal. Assisted by Matt Ritchie with a cross.
Corner,  Newcastle United. Conceded by Neil Taylor.
Corner,  Newcastle United. Conceded by Sam Johnstone.
Attempt saved. Matt Ritchie (Newcastle United) left footed shot from the left side of the box is saved in the top centre of the goal. Assisted by Paul Dummett.
Attempt saved. Birkir Bjarnason (Aston Villa) right footed shot from the centre of the box is saved in the centre of the goal.
Foul by Mohamed Diamé (Newcastle United).
Jonathan Kodjia (Aston Villa) wins a free kick in the defensive half.
Own Goal by Henri Lansbury, Aston Villa.  Newcastle United 2, Aston Villa 0.
Attempt blocked. Jamaal Lascelles (Newcastle United) left footed shot from the left side of the six yard box is blocked. Assisted by Jonjo Shelvey with a cross.
Corner,  Newcastle United. Conceded by Henri Lansbury.
Corner,  Newcastle United. Conceded by Sam Johnstone.
Attempt saved. Jonjo Shelvey (Newcastle United) right footed shot from outside the box is saved in the bottom left corner.
Mohamed Diamé (Newcastle United) wins a free kick in the attacking half.
Foul by Mile Jedinak (Aston Villa).
Attempt blocked. Jonathan Kodjia (Aston Villa) right footed shot from outside the box is blocked. Assisted by Conor Hourihane.
Attempt missed. Birkir Bjarnason (Aston Villa) right footed shot from outside the box is high and wide to the right following a set piece situation.
Foul by Yoan Gouffran (Newcastle United).
Alan Hutton (Aston Villa) wins a free kick in the attacking half.
Foul by Aleksandar Mitrovic (Newcastle United).
James Chester (Aston Villa) wins a free kick in the defensive half.
Attempt blocked. Birkir Bjarnason (Aston Villa) left footed shot from outside the box is blocked.
Foul by DeAndre Yedlin (Newcastle United).
Henri Lansbury (Aston Villa) wins a free kick in the attacking half.
Newcastle United scored a goal in each half to beat Aston Villa and go a point clear at the top of the Championship.