Right-back Lowton broke the deadlock on Saturday with a 20-yard first-half volley and substitute Benteke wrapped up the points with two minutes left.
It was another encouraging performance from a new-look Villa side being assembled by Paul Lambert after their 1-1 draw at Newcastle.
Lambert had promised to entertain and this Villa side look more likely to create opportunities than the dour football served up under former manager Alex McLeish.
Another newcomer in winger Brett Holman caused problems but of equal encouragement was the solid look about the back four in which keeper Brad Guzan and centre-back Ciaran Clark were outstanding.
After a promising start, the Swans seldom looked like adding to the 10 goals netted in their opening three games despite the promptings of Jonathan De Guzman in midfield.
Villa started on the offensive and a shot on the turn from Andreas Weimann was blocked by Alan Tate.
But Swansea were soon into their stride and Clark produced two fine tackles to halt runs from Danny Graham and Nathan Dyer.
It needed two superb reflex saves in the space of 60 seconds from Guzan, again preferred to Shay Given, to prevent Swansea from breaking the deadlock.
First the United States international reacted quickly to turn over a powerful close-range header by Ashley Williams from a De Guzman corner.
Then Guzan went full length to finger-tip a dipping 20-yard drive from Dyer over the bar.
Villa retaliated and a superb strike from Lowton put them in front after 16 minutes.
Ben Davies was forced to concede a corner after a good move involving Holman, Stephen Ireland and Darren Bent.
Barry Bannan's resulting cross was headed out by Williams but Lowton brought the ball under control and volleyed an unstoppable shot past Michel Vorm from just inside the area.
Clark became the first player to be yellow-carded after lunging in at Swansea defender Angel Rangel.
Lowton and Miguel Michu were also cautioned for fouls on Ben Davies and Eric Lichaj respectively.
Vorm reacted sharply to turn aside a first time attempt from Andreas Weimann after being set up by Bent.
But on the stroke of half-time Graham failed to make contact with a low cross from Dyer with the goal at his mercy after a late run into the danger area.
Swansea were having problems coping with set pieces and a Bannan corner at the start of the second period found its way to Clark at the far post and his shot struck the legs of Vorm.
Leon Britton then headed a Weimann shot on the turn off the line after the visitors failed to deal with another Bannan centre.
Lambert was increasingly animated on the touch-line reminiscent of the manager he calls 'gaffer' in former Villa boss Martin O'Neill.
Villa's £7million transfer deadline day signing, Benteke, came on for Weimann and instantly had a shot deflected wide.
Bannan's corner again troubled the Swans with Clark's header tipped over by Vorm.
Villa ended on top and Karim El Ahmadi was denied by Vorm before Benteke wrapped up the points.
Williams headed back pass fell short of Vorm and Benteke nipped in to lob the ball over the keeper before applying the finishing touch.