The 30-year-old has been dropped by interim manager Gareth Southgate for Tuesday's World Cup qualifier against Slovenia, the first time he's been left out of the lineup since the final group game of Euro 2016.
"It's a very straight forward decision," Southgate said at Monday's press conference in Ljubljana. "We've looked at the way Slovenia played last week and we knew the profile of midfield we wanted to play.
"In no way is it a reflection of his performance on Saturday (against Malta), he played well and dictated play with discipline, but we felt it was the right decision."
Rooney's recent performances have come under scrutiny from large sections of the media, as well as Manchester United and England fans.
The United captain has one goal in 12 appearances for club and country this term, scoring on the opening weekend of the Premier League season.
Manchester United manager Jose Mourinho has already left Rooney on the bench for two consecutive Premier League matches -- the 4-1 win over Leicester
and a 1-1 draw with Stoke.
Southgate revealed he initially had reservations about Rooney attending the press conference with him as it would invite further media attention, but the player insisted.
"Of course you want to play, but I understand and respect the manager's decision," Rooney said. "I'll support the players 100% and try and help the players get the points tomorrow.
"I'll be ready to come off the bench if needed -- again I show great pride in playing for my country, I love playing for my country."
Southgate recently called some of the criticism of Rooney "unfair," while England teammate John Stones admitted he was "shocked" by the audible boos aimed at Rooney following the 2-0 victory against Malta.
"To be honest I wasn't aware of it at the time," Rooney said of the jeers at Wembley. "I think football nowadays is like that sometimes, that's part of the game but I wasn't aware of it on the pitch."
Southgate confirmed Rooney will remain England captain, though Liverpool midfielder Jordan Henderson will wear the armband against Slovenia.
"When you have a difficult conversation with a young player, I think coaches around the country will say, 'That's the way the England captain dealt with that situation,'" Southgate said of Rooney's status in the team setup.
"I think there's been a depth to his leadership that people from outside the group unfortunately won't be aware of, he's almost like a coach within the dressing room already.
"That's a huge compliment to his footballing intelligence, but he's got a a lot of football in him to play."
Though England sits top of Group F after wins against Slovakia and Malta, the national team has been making headlines off the pitch rather than on it.
Former manager Sam Allardyce was sacked after just one game
and 67 days following an undercover sting by a British newspaper, seemingly admitting that he knew of ways to skirt FIFA rules on player ownership.
Allardyce replaced Roy Hodgson after England suffered a shock loss to Iceland
in the last 16 at Euro 2016 in France.
Southgate was promoted from England U21 manager to take charge of the remaining four games of 2016, as the FA searches for a permanent replacement.
Slovenia is third in the group, behind Scotland on goal difference. It beat Slovakia 1-0 on Saturday, having drawn 2-2 with Lithuania last month.