Rooney fired the Three Lions ahead in just the sixth minute in Podgorica, nodding home from Steven Gerrard's corner to mark his 35th goal for his country.
But England unravelled in the second half as Montenegro came out fighting and were pegged back by substitute Dejan Damjanovic's equaliser in a 1-1 draw.
Manchester United striker Rooney believes England will learn from that collapse, with the pressure on Roy Hodgson's side now even greater ahead of the final round of qualifiers later this year.
He said: "We still have a great chance of qualification.
"It was a lesson for us in the second half and we need to learn how to see out these games better.
"You can't regret anything. It's just the way the game's gone and we have to accept it.
"A point was probably a fair result though we're disappointed we didn't get three.
"But credit to Montenegro, they came back, had a go and put us under a lot of pressure, especially off the set-pieces."
While disappointed by the draw, Rooney admits he is pleased with his individual scoring form, having now scored six in his last five appearances for England and four in as many games in all competitions.
"I'm enjoying my football," added the 27-year-old. "It's been probably my best run since I've been playing for England."