The result returned Hamilton to the top of the World Drivers' Championship standings with 182 points, three ahead of the previous leader Webber in second.
Webber's teammate Sebastian Vettel remained in third despite coming 15th after colliding with Jenson Button and sustaining a left-rear puncture from contact with Vitantonio Liuzzi's Force India car.
La Source turn had a larger area of artificial grass and a 50 mm (2.0 in) kerb installed at the corner to deter competitors from transgressing track limits.
[9][10] Although he had reclaimed the World Drivers' Championship lead from Hamilton in Hungary, Webber said consistently finishing and reliability was an important factor in the final seven races, "You have to be mindful of the fact that you might not get anything out of it so you need to realise that four points is better than none and gambling.
"[7] His teammate Vettel, the bookmakers' favourite for victory,[11] said his title challenge would commence in Belgium following reliability issues and incidents losing him points in past events, "We have to focus on each and every race.
[15] The team also added a modified diffuser and floor to maximise the F10's performance within FIA compliance restricting the size of the car's lower surface to reduce the downforce generated.
[2] Renault introduced a version of McLaren's F-duct tool to their R30 car activated by the driver's left hand and directed air to the main section of the rear wing instead of the flap.
Hamilton, Renault's Robert Kubica, Vettel, Sutil, Button, Webber, Kamui Kobayashi of Sauber, Williams' Rubens Barrichello, and Mercedes' Michael Schumacher made up positions two through ten.
Children were reportedly climbing the catch fence on track grounds, forcing FIA race director Charlie Whiting to drive the safety car and do an inspection.
While the session restarted with four minutes left, a malfunctioning red light delayed on-track action, requiring marshals to wave a green flag to resume proceedings.
[20] Qualifying commenced in clear weather before rain showers fell on parts of the circuit, making the surface uneven and catching some drivers out.
[33] Button took fifth by saving a set of soft tyres despite losing time through an error at La Source turn and being circumspect at Fagnes corner.
[33] Lotus' Jarno Trulli, 18th, made contact with the right-rear of Lucas di Grassi's out of control Virgin Racing vehicle at Stavelot turn.
[29][33] Vitaly Petrov lost control of his Renault on dry tyres on a damp kerb exiting Rivage corner and spun into the inside barrier backwards.
[4][45] The rain showers observed in the morning's support events altered the level of grip,[44] and tyre strategy had the potential to effect the final finishing order according to Sarah Holt of BBC Sport.
[2] Before the start, Massa was observed by amateur video footage posted on the internet to have transgressed sporting regulation by being slightly out of position on the grid.
Sutil clung onto Webber's slipstream and overtook him on the straight for sixth before losing the place by running wide into Les Combes corner.
[48][51] The rain shower made the back of the track damp through Blanchimont corner and the conditions caused several drivers to run wide at the Bus Stop chicane due to a loss of grip braking for the turn.
[2][48][49] Button attempted to pass Kubica on the outside but sustained left front wing damage affecting its aerodynamic balance as it became apparent several drivers could not turn into the chicane and drove onto the run-off tarmac.
[2][49] Sutil's higher straightline speed moved him past Hülkenberg for seventh to nullify an earlier illegal pass by the latter on the former at the Bus Stop chicane.
[2] Button's handling difficulties caused by front wing damage allowed his teammate Hamilton to pull away from the rest of the field to be 4.8 seconds ahead by lap seven.
[46][48] On lap six,[44] Senna, nursing front wing damage,[50] drove slowly into the pit lane to retire with rear-left suspension failure that caused him to spin.
Vettel suddenly switched to the outside line and lost control of his car by hitting a bump on the damp circuit as he was unable to correct an opposite lock at high speed.
[51] Alonso ran wide on the paint marking the outside kerb exiting Les Combes turn and into Malmedy corner and lost control of his car.
The Mercedes pair of Rosberg and Schumacher finished sixth and seventh following the team's decision to keep their drivers on track for longer and were just more than a second ahead of eighth-placed Kobayashi.
Glock in 18th lost performance on a set of full-wet tyres before the second rain shower and ran a new front wing after demolishing a brake marker board on lap one.
[3][20] Hamilton described it as "a very, very tough race" for himself and said the victory "absolutely" made up for two years prior, adding: "At the end it was just about nursing the car home and bringing it back in one piece.
"[55] Kubica stated he did not believe others would think Renault would be competitive in Belgium and noted their results in each of the sessions, adding: "It was a very tricky race but we've seen very good pace.
"[56] Button described the crash as "a strange incident and so sad because I was fighting for second position", adding: "I defended my line about three inches on the inside and perhaps Sebastian got confused as to which direction to go...
"[62] The stewards added 20 seconds to Alguersuari's overall race time in lieu of a drive-through penalty after deeming him to have illegally cut the Bus Stop chicane to pass Liuzzi for tenth on lap 42.