The goal was Rooney’s 44th for his country and drew him level with Jimmy Greaves as England’s joint-third highest all-time scorer.
Only Gary Lineker on 48 goals and Bobby Charlton on 49 stand above him on the all-time list and with age on his side, the 29-year-old should become the first Englishman to score 50 goals for his country.
Charlton, who scored his last England goal in 1970, presented Rooney with a symbolic golden cap before the game, which only came to life in the second half after a turgid opening 45 minutes.
“It was a good day in the end,” Rooney told ITV.
“We had to show character and that will be good for us in the team. Since the World Cup we haven’t faced that.”
England looked poor in the first half and not much better until Jordan Henderson put through his own goal to give Slovenia the lead in the 57th minute. That sparked the home side into life.
“It really woke us up and we went and showed what a good side we are. For the penalty I was trying to get a yard and I was clipped, it was a clear penalty,” Rooney said.
Rooney thundered the ball home and although Slovenia keeper Samir Handanovic did get a touch on the ball, he was powerless to stop it going in.
Rooney, who turned 29 last month, became the ninth player to join England’s 100 club which is headed by Peter Shilton, who won the last of his 125 caps in 1990.
Rooney became the youngest player to represent England at the time of his debut aged 17 years and 111 days against Australia on Feb 12, 2003.
He then became the youngest player to score for England in a 2-1 win over Macedonia in a Euro 2004 qualifier in Skopje, aged 17 years 317 days.
Although Theo Walcott eclipsed his youngest appearance record in 2006, Rooney’s record as youngest scorer still stands and he now has Charlton’s all-time record well within his sights.
(Editing by Ed Osmond)