Eden Hazard struck the only goal just after the hour as Belgium followed up their 2-0 away win over Macedonia on Friday with another triumph.
That lifted them onto 16 points at the top of Group A but they only remain ahead of Croatia on goal difference after their rivals fought back from a goal down to beat Wales 2-1 tonight.
Marc Wilmots' side dominated the opening period in Brussels but were frustrated in their bid to find the breakthrough.
Eden Hazard and Kevin De Bruyne, Belgium's goalscorers in Skopje, both went close in the opening 20 minutes, the former being denied by Tome Pacovski before De Bruyne fired inches wide of the far post.
Hazard and Dries Mertens then tried their luck without success before Thomas Vermaelen got the ball into the net only to see his effort ruled out for offside.
Belgium's final chance of a one-sided first half fell to De Bruyne but the winger's shot from the edge of the box went wide.
Macedonia, whose only real threat on goal before the break saw Goran Pandev fail to seriously trouble Thibaut Courtois, found themselves on the backfoot again immediately after half-time with Vermaelen heading wide from a Hazard corner.
The hosts survived a brief scare when Nikolce Noveski headed a decent opening over from a free-kick before resuming their offensive on the Macedonia goal with fit-again Vincent Kompany seeing his 55th-minute header from another Hazard corner parried away by Pacovski.
Hazard, inevitably, was proving a real menace to Macedonia and he almost broke the deadlock in the 59th minute with a shot from the edge of the box that crashed against the woodwork.
The Chelsea playmaker did not have to wait much longer to get his name on the scoresheet, though, as three minutes later he fired Belgium ahead with a neat left-footed finish.
That proved to be the match-winner as although Macedonia tried to mount a fightback in the closing stages, with Pandev, Nikola Gligorov and Aleksandar Trajkovski seeing efforts go wide, they could find no way through.