Gibbs (right) scored past both goalkeepers as goals flew in
West Ham's Zavon Hines scored twice on his U21 debut as England won their first home European qualifier in style.
Kieran Gibbs nodded home from Arsenal team-mate Theo Walcott before Micah Richards' header doubled the lead.
Muarem's free kick pulled one back for Macedonia and Agim Ibraimi coolly levelled soon after the break.
Andy Carroll glanced England back ahead then Gibbs sent a corner past his own keeper, but two simple Hines strikes and Carroll's low shot sealed victory.
Opponents Macedonia refused to lie down until late in the game, despite going 2-0 down early on.
And, despite the convincing scoreline, questions will be asked of the young England side's defending.
The home side survived early pressure at Coventry's Ricoh Arena, and midway through the first half Gibbs was able to head into an empty net after Walcott had beaten goalkeeper Kristijan Naumovski.
England looked to be pulling clear when Manchester City defender Richards met a Michael Mancienne flick-on from a corner, but Maurem's low free-kick somehow evaded a sea of legs to nestle behind Scott Loach in the England net.
That gave Macedonia hope going into the break, and they were level only eight minutes into the second half, thanks to more poor defending from England.
Mancienne slipped to allow Ibraimi through on goal, the 21-year-old curling his finish past the flailing right glove of Loach.
England were back in front within moments as Gibbs, with a goal to his name, turned provider, holding off a succession of challenges on the left wing before delivering a cross for Newcastle striker Carroll to divert home.
But the Arsenal defender's joy turned to misery as he lashed his left leg at a low Macedonia corner, angling the ball past his own goalkeeper to level the game.
However, Hines, who had replaced Walcott at half time, soon had England back in front.
The 20-year-old, no stranger to the Ricoh Arena as a former Coventry loanee, latched on to a Tom Cleverley through ball, ignored a queue of team-mates in front of goal to score himself.
England had several glorious opportunities to make sure of the win, including one astounding miss where no less than four England strikers failed to convert past the helpless Macedonian goalkeeper, before Carroll scraped the ball in from 15 yards.
Hines finished off Macedonia with his second, and England's sixth, a close-range volley late in the game.
Arsenal will be keen to check on the fitness of Walcott, who did not reappear after the break having suffered a dead leg, while Manchester City defender Richards was clattered by team-mate Fabrice Muamba.
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