Roy Hodgson's side looked set to cruise to victory after the Manchester United forward scored to give England a sixth-minute lead in Podgorica, but the visitors were forced to hold on after conceding a late equalizer.
The 27-year-old Rooney believes the setback will set up the Three Lions for success in the rest of their qualifying campaign, with three of their four remaining games coming at Wembley Stadium.
"We still have a great chance of qualification," Rooney told reporters. "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."
Rooney's goal against the Montenegrins was his 35th for England and sixth in his last five games at international level.
"It's been probably my best run since I've been playing for England," Rooney said.