Zlatan Ibrahimovic struck a brace as Sweden beat Montenegro yesterday but Russia were the day's big losers, a defeat to Austria coming as a blow to their prospects of reaching the finals in France in a year's time.
England are on a fast track to Euro 2016 having won six games out of six in qualifying Group E, although they needed an 86th-minute winner from Rooney to secure victory in Ljubljana.
Slovenia substitute Nejc Pecnik appeared to have rescued a point with an 84th-minute equaliser, but moments later Rooney atoned for two glaring earlier misses by scoring his 48th England goal, taking him level with Gary Lineker and leaving him one goal behind all-time leading scorer Bobby Charlton.
"It's great to score the winner, but it was a great team performance," captain Rooney told ITV.
England are six points clear at the top of the section from Switzerland, who came from behind to beat Lithuania 2-1 in Vilnius.
In the group's other game, Sergei Zenjov scored two goals either side of half-time as Estonia defeated minnows San Marino -- England's next opponents in September -- 2-0 in Tallinn.
Meanwhile, Euro 2008 and Euro 2012 winners Spain made it five victories from six games in Group C by beating Belarus 1 -0 at the Borisov Arena in Barysaw.
Manchester City's David Silva got the only goal of the game in Vicente del Bosque's 100th match in charge of La Roja, controlling a Cesc Fabregas free-kick at the back post and volleying in.