The Manchester United captain marked his first fixture as England captain with a powerful 68th-minute spot-kick, awarded by Portuguese referee Jorge Sousa when Raheem Sterling was brought down in the box by Omar Elabdellaoui.
However, Rooney's penalty was one of only two shots on target from Roy Hodgson's men in the course of 90 minutes, and the crowd of 40,181 - the lowest for a full international since Wembley reopened in 2007 - received little in the way of entertainment value, or encouragement after the short World Cup campaign in Brazil.
The visitors enjoyed a threatening spell at the start of the second half, with Joe Hart having to make an excellent diving save to his left to thwart a Josh King header from a corner.
Liverpool winger Sterling was by far the pick of the players on show, linking up dangerously on occasions with his club colleague Daniel Sturridge.
England next move on to Basel for their European Qualifiers Group E opener against Switzerland on Monday night.
Hodgson may have to shuffle his pack for that game as Gary Cahill came off late on with an ankle problem.
In the opening stages, Per Ciljan Skjelbred brought Jack Wilshere down after he played a clever one-two with Jordan Henderson in the fourth minute.
The supporters were hush with anticipation as Leighton Baines stepped up to strike the ball, but the Everton left-back's curling effort flew five yards over.
The disappointing effort set the tone for what ended up being a dour first half. Norway broke up England's tentative attacks by any means. Skjelbred knocked Wilshere off the ball as he approached the box and the Norway captain stopped Baines in his tracks with a flying elbow.
Sturridge and Sterling were the only lights to brighten up the first period. Sterling backheeled the ball into Sturridge's path, but the striker's shot was blocked inside the box.
Sturridge then cushioned a 40-yard diagonal pass from Sterling, but goalkeeper Orjan Nyland pressured the striker into lobbing over the bar.
Unlike England, Norway managed to register a shot on target, although it was a tame one from Tarik Elyounoussi, who volleyed straight at Hart.
England thought they should have had a penalty towards the end of the first half when Havard Nordtveit put in a late tackle on Wilshere, but the referee waved play on.
Then, in the final minute of the half, Hart carelessly spilled Skjelbred's cross, almost dropping the ball into his own net.
A few dissenting voices were heard at the half-time whistle. If the fans inside the stadium were hoping for an instant improvement after the restart, then they were to be disappointed.
The Three Lions were just as slow in their build-up play and they were very flat at the back.
Hart saved a low drive from Mats Daehli and the England goalkeeper managed to deny King with an acrobatic dive.
Some sloppy defending from Cahill allowed King to race into the box, but he could not convert.
England were thrown their chance to forge ahead in the 68th minute when Elabdellaoui slid in late on Sterling and the referee pointed to the spot.
Rooney stepped up and launched the ball past Nyland with his right foot.
The goal released the pressure and England finally started to play with attacking intent.
Danny Welbeck, who came on for Rooney, drew a good save from Nyland.
Fabian Delph and Calum Chambers came on for their debuts and Cahill went off to receive ice to his foot.
The game petered out and those that had remained in the stadium for the final whistle greeted the end with barely audible cheers.