The 32-year-old, who has 14 FIFA World Cup goals to his credit and is just one away from matching Ronaldo's all-time record, scored his 53rd goal for his country on his 102nd appearance.
Despite clinching three points, Joachim Low's Germany, who finished third in South Africa, are second in Group A behind Turkey after Guus Hiddink's side had earlier won their opening qualifier 3-0 in Kazakhstan.
The Germans were at virtually full-strength at the Stade Roi Baudouin and were made to work hard for the victory as Belgium, led by Arsenal defender Thomas Vermaelen, battled hard throughout.
With Michael Ballack working his way back to fitness after the ankle injury which kept him out of the World Cup, Bayern Munich's Philipp Lahm captained Germany at right-back with Hamburg's Marcell Jansen on the other flank.
In attack, Low named World Cup top-scorer Thomas Mueller, Mesut Ozil with Klose as the lone striker.
Belgium coach Georges Leekens chose experienced centre-backs Daniel van Buyten of Bayern Munich and Manchester City's Vincent Kompany while in attack 17-year-old Romelu Lukaku of Anderlecht was the lone striker.
The Belgian side had an average age of just 24 years, four months with Lille's 19-year-old Eden Hazard on the left wing, with Germany at 25 years, one month on average as both sides look to the future.
Belgium had the better of the chances in the opening spell as Lukaku went one-on-one with goalkeeper Manuel Neuer on 11 minutes.
Kompany picked up the first yellow card when he sent Klose crashing to the turf after 12 minutes, but Bastian Schweinsteiger was wide of the mark with his free-kick. Lukaku then beat Badstuber and Jansen out on the right, but Everton's Marouane Fellaini failed to connect with his shot on 14 minutes.
With Germany becoming frustrated, Schweinsteiger picked up a yellow card just before half-time after he went too high into a tackle on Belgian midfielder Jan Vertonghen.
The guests took the lead when Mueller capitalised on a mistake in the Belgian defence to thread a pass through to Klose who slotted past Belgium goalkeeper Logan Bailly on 51 minutes.