Georgi Hristov gave Macedonia a 28th minute lead, but 17-year-old Rooney became England's youngest goalscorer with a fine 53rd-minute equaliser and captain Beckham slotted home 10 minutes later.
"This was the important one," Beckham told Sky Sports television. "I'm not sure we deserved to be 1-0 down but it was character again that brought us through in the second half."
England's seventh straight victory, equalling their post-war record, lifted them to provisional top spot in Group Seven on 16 points, one ahead of Turkey, who were playing later in Liechtenstein.
It meant that, assuming England beat Liechtenstein next Wednesday at Old Trafford, Sven-Goran Eriksson's side will only need a draw in their final qualifier in Turkey next month to book their place at next year's tournament.
However, the win was marred by racist abuse for England substitute Emile Heskey and occasional unrest in a crowd where several hundred England fans, who had defied Football Association (FA) calls not to travel, were mixed with the home supporters.
DIFFERENT PERFORMANCES
On the pitch, England put on two markedly different performances, bitterly disappointing in the first half, but inspired in the second after a tactical switch by coach Sven-Goran Eriksson.
Sorely missing the midfield authority of Steven Gerrard and creative spark of Paul Scholes due to injuries, England were also let down by near-comic book defending.
Skipper Artim Sakiri, who scored direct from a corner in a 2-2 draw last October, was the architect of Macedonia's attacks, spraying passes for strikers Ilco Naumoski and Hristov.
Neither side had created a clear chance, though, until the 28th minute when defender Sol Campbell failed to clear Vlatko Grozdanovski's cross from the right, England tried to scramble the ball away but it ran for Hristov, who squeezed a shot past goalkeeper David James.
England showed more purpose going forward but Macedonia's well drilled defence and a very mobile midfield were quick to smother any danger.
Beckham, booked for a foul as the frustration began to build, tried his luck with a long-distance free kick in stoppage time, which Petar Milosevski comfortably gathered.
It was England's only real attempt on target, prompting Eriksson to switch from the usual 4-4-2 to 4-3-3 for the second half by replacing midfielder Frank Lampard with striker Heskey.
The change soon paid dividends, Rooney levelling within eight minutes when he fired home a low shot from the edge of the area after Heskey nodded down a long ball from Beckham to become England's youngest ever goal-scorer.
Rooney, aged 17 years 317 days, beat the record set by his team mate Michael Owen, who was 18 years and 164 days old when he scored against Morocco in May 1998.
England kept pushing for a second goal and soon found it when defender John Terry was tripped by Macedonia's Brazilian-born substitute Braga and Beckham converted the penalty.
Eriksson's men nearly snatched a third when Campbell had a glancing header parried and Owen's follow-up shot failed to beat Milosevski.
The FA had not used its ticket allocation for England fans, fearing any repeat of crowd trouble in April's win over Turkey in Sunderland that could lead to England being excluded from next year's championship in Portugal.
Macedonia fans burned an England flag and booed the British anthem minutes before kickoff.
