Clyne won his first two England caps against Slovenia and Scotland during the recent international break and the right-back was the man of the moment for Southampton as well thanks to his crucial 81st minute strike at Villa Park.
Ronald Koeman’s second placed side looked set for only their third defeat in the Premier League this season after Gabriel Agbonlahor put struggling Villa ahead following a mistake by Saints goalkeeper Fraser Forster in the first half.
But Clyne’s third goal of the campaign ensured Southampton, the season’s surprise success story, survived to extend their unbeaten run in all competitions to six matches and move within six points of leaders Chelsea.
In contrast, lowly Villa are without a win in their last eight league games and Paul Lambert’s team are just two points above the relegation zone.
“I didn’t come for one point but we didn’t create as many chances as we should have and we missed some fitness and some quality,” Koeman said.
“The goal was a misunderstanding defensively but we are human so we can make those mistakes.
“Every game is a battle and tonight was difficult. We did not reach our level.”
The subdued atmosphere created by the lowest league crowd at Villa Park since 1999 suggested the home fans didn’t fancy their team’s chances and it was Southampton who almost seized the early lead with Kenya midfielder Victor Wanyama sweeping over from the edge of the penalty area.
But Villa took the lead against the run of play in the 29th minute.
Ciaran Clark’s long clearance should have been dealt with easily but England international Forster needlessly rushed out of his goal and Agbonlahor surged ahead of Jose Fonte, beat him to the ball and fired into the empty net.
It was the first goal Southampton had conceded in seven and a half hours of game time, and the shock sparked them back into action.
Villa goalkeeper Brad Guzan had to tip Sadio Mane’s curling effort around the post on 37 minutes.
Fonte then headed straight at Guzan as the visitors threatened an equaliser before the interval.
Southampton were almost 2-0 behind two minutes into the second half, though, when Ryan Bertrand hacked Charles N’Zogbia’s goalbound effort away.
Andreas Weimann wasted a golden chance to seal the points with 12 minutes left when he broke from Southampton’s corner.
The Villa forward found Agbonlahor and received the return pass in clear sight of goal, but could only blaze over from 12 yards.
And Villa paid the price when Saints levelled with nine minutes remaining.
Bertrand got the better of Weimann and his left-wing cross was met by Clyne’s cool finish.