On a night when Darren Bent was once again overlooked and reduced to the role of watching from his executive box, Christian Benteke's towering header 10 minutes from time secured Aston Villa a precious three points that lifts them out of the relegation zone and leaves Reading second from bottom.

With the clock ticking down and Villa seemingly running out of ideas, the sense of relief inside this stadium was palpable when Benteke, who has effectively replaced Bent up front, registered his fifth goal since arriving from Genk for £7m in August. The Belgium international celebrated on his knees, the manager, Paul Lambert, leapt off the bench and the Holte End rejoiced in a goal that delivered only the third home league win they have witnessed in 12 months.

With three out of their next four league matches away, including a trip to Loftus Road to face bottom-of-the-table Queens Park Rangers on Saturday, this was a hugely significant result for Lambert, even if only 28,692 turned up – the lowest Premier League crowd at Villa Park in almost six years.

Until the moment Benteke scored Lambert's decision to jettison Bent for the second time in four days had looked like coming under increased scrutiny. Villa deserved to win on the balance of play but it was impossible not to wonder what was going through Bent's mind as he looked down from his seat in the Trinity Road stand and watched chances squandered, in particular the one Andreas Weimann blazed over the bar early in the first half from Benteke's screwed centre.

Although there were reports beforehand that Bent had stormed out and left the ground after Lambert read out the team, it emerged that the striker had gone to his car before returning to watch the game. It is not so much Lambert's decision to start without Bent which is strange but the fact that he is selecting Jordan Bowery, a 21-year-old striker signed from Chesterfield in the summer who has seven minutes of top-flight football to his name, on the bench ahead of a player who has scored 102 Premier League goals.

In between trotting out the familiar line about "doing the most important thing for the football club", Lambert denied that he had any problem with Bent, insisted that he rated him as a player and claimed he had no issue with the centre-forward's application in training or in relation to his attitude. There was, though, a clear sense of vindication in his demeanour in terms of Benteke scoring the winner.

"I'll always make decisions that I think are right for this club and I'll live or die by them," the Villa manager said. "That's the nature of the beast."

For Reading, who started the game one place and one point behind Villa, a worrying pattern is starting to emerge in terms of games slipping from their grasp as a result of conceding late goals. They have now shipped 16 in the final half-hour of matches – more than any other Premier League club this season – and Brian McDermott acknowledged that record needs to be addressed if they are to give themselves a fighting chance over the remainder of the campaign. "It's frustrating to lose another one late," Reading's manager said. "It's all about trying to solve that issue."

Although Villa enjoyed greater possession and created more chances – Benteke and Nathan Baker went close in the first half but the former's shot lacked power while the latter misdirected his header from Barry Bannan's corner – Reading were not without their own opportunities.

The best of them fell to Adam le Fondre, who was unable to make a decent connection with an overhead kick inside the six-yard box in the 10th minute and wasted a free header on the hour mark, from a similar position, following Nicky Shorey's corner. "I didn't think we were going to lose the game at any point and I thought we were going to nick a goal but unfortunately they did," said McDermott.

A Villa side with an average age of 23 years and 324 days – their youngest ever starting XI in the Premier League – were getting a little desperate but the breakthrough arrived when Benteke climbed above Sean Morrison to head home Ashley Westwood's corner and enhance his burgeoning reputation.

"I'm running out of things to say about the big guy," Lambert said. "He's turned himself into a fans' favourite here. I thought the header was fantastic. But I think his general game has been great. You almost forget he's only 21 years of age and he might not hit his peak until his late 20s."