The victory, which cements England’s lead at the top of their Euro 2016 qualifying group, meant England ended the season unbeaten for the first time in 24 years.
Wilshere’s two goals — in response to Milivoje Novakovic’s opener — put England ahead for the first time, but Nejc Pecnik stepped off the bench to score what he thought was an equaliser six minutes from time.
Two minutes later, shortly after receiving an elbow in the face from Bostjan Cesar, Rooney kept his nerve to capitalise on a mistimed tackle from Bojan Jokic and slide the ball past Samir Handanovic.
PHOTO: Cheers skip! England captain @WayneRooney celebrates his winner in Slovenia #SvnEng pic.twitter.com/qHMp5Un431
— England (@England) June 14, 2015
The winning goal put Rooney just one goal shy of Sir Bobby Charlton’s 49-goal record and his manager could not have been happier for him.
Welcome to the 48 club @WayneRooney . And thank you for making young folk aware that I once played a bit and don't just flog crisps.
— Gary Lineker (@GaryLineker) June 14, 2015
“Wayne Rooney’s performance says a lot of things about him as a man,” the England manager said of his captain.
“Just before he took that chance he took a nasty blow from an elbow, which could have decked many a player and led to him losing his discipline. It didn’t and he got up. He had one or two chances that had gone begging, but when the ball fell to him he still stuck it away with aplomb.
“We can rely on that man. I’d have liked him to get a hat-trick today so all the talk of the record would be finished, but he has plenty of time.”
Rooney ended the season with 22 goals. He said: “It’s great to score the winner and it was a great team performance.”
It has taken five years for Wilshere to break his duck with England. His first was a fierce arrow into the far corner after a poor clearance. The second was the pick of the pair. Henderson played the ball into Adam Lallana, who flicked the ball into Wilshere’s path and he let fly with a drive into the top right-hand corner.
Roy Hodgson: "Both of @JackWilshere's strikes were fantastic and really summed up his game" http://t.co/heSimBsAHZ pic.twitter.com/4ebggK98pG
— England (@England) June 14, 2015
“His whole performance was quality,” Hodgson said of the Arsenal midfielder. When asked if it was the best goal he had seen in his three-year tenure as England boss, Hodgson said: “It’s always the last one which excites me the most. I’d have to have all the goals put before me [to make a decision]. I remember Andy Carroll’s bullet header (in Euro 2012), but I’m very happy with Jack, the goals he’s scored and his performance.”
England have won eight and drawn two since the World Cup. Reflecting on going the season unbeaten, Hodgson said: “It’s a good achievement. That’s not been done for over 20 years. The players deserve some credit for that.”
Handanovic, Brecko, Ilic, Cesar, Jokic, Ilicic (Birsa 61), Mertelj, Kurtic (Lazarevic 79), Kampl, Kirm (Pecnik 72), Novakovic
Hart, Jones (Lallana 45), Cahill, Smalling, Gibbs, Henderson, Wilshere, Delph (Clyne 85), Townsend (Walcott 74), Rooney, Sterling
A Undiano Mallenco (Spain)