Milivoje Novakovic capitalised on confusion in the England defence to give Slovenia a half-time lead in Ljubljana but Wilshere twice found the net from long range to turn the Euro 2016 qualifier on its head before Nejc Pecnik and Rooney both scored in a breathless finale.
The result sees England stretch their lead at the top of Group E to nine points on the road to France next summer and also finish a season unbeaten for the first time in 24 years.
"He's been fantastic," Rooney told ITV when asked about Wilshere's performance.
"Jack and myself have formed a good understanding on the pitch when he's in that deeper role. He's still learning, he's a young player but it's a new role that he's taken in his stride.
"Hopefully he's injury free because he will be a top player in world football."
Wilshere's first goals for England provided the exclamation points on an all-action display at the base of midfield and boss Roy Hodgson also had words of praise for his overall performance.
"They weren’t exactly tap-ins!" he said of the goals. "Both strikes were fantastic and really summed up Jack’s game - in particular in the second half when he really took over the midfield.
"It’s good to see that’s he’s not only creating chances for us and doing his work defensively, he’s also chipping in with two very important goals which put us on the front foot after coming in on the back foot at half-time."