That meant his main hope of holding off the Ferrari driver was to build a lead big enough before his stop on lap 10 that Raikkonen could not close it on his extra lap.
Instead, although Hamilton shadowed Raikkonen to the first stops, he could not pass him.
Hamilton's hopes were further dented when he came out from his pit stop right behind his slower team-mate Heikki Kovalainen, who was battling for position with Kubica.
By the time he had cleared Kovalainen and Kubica five laps later, Raikkonen was five seconds ahead, a lead he was able to maintain comfortably to the second round of stops.
The two men both made their final stops on lap 25 and on the harder tyre Hamilton was able to close on the Ferrari.
The 23-year-old shaved about half a second a lap out of Raikkonen's lead and was within two seconds of the Ferrari by lap 31.
Raikkonen's hopes of victory - and probably the title - ended with a crash
He was unable to make much more of an impression until the predicted late shower of rain arrived with about five laps to go.
Within minutes, the back of the circuit was soaking, while it remained dry in the vicinity of the pits - not an unusual situation at a track renowned for its capricious weather.
Hamilton closed right up to Raikkonen on lap 42 but he fatefully cut the Bus Stop chicane after pulling out of a passing move at the end of the lap.
He then chased Raikkonen down the pit straight and passed the Ferrari going into the La Source hairpin at the start of lap 43.
But that was not the end of the battle.
When the two men reached the wet part of the track halfway around the lap, Hamilton slid off, handing the lead back to Raikkonen, who almost immediately lost it again by sliding off himself.
The Finn then lost control going through the fast Blanchimont corner, and speared into the wall.
But the drama had not finished, and was merely switched to the stewards' office.
Their decision is likely to be greeted with cynicism as it makes the championship battle dramatically closer at a time when Hamilton was beginning to look like he was inching towards his first title.
Result of Belgian Grand Prix:
1. Felipe Massa (Brz) Ferrari one hour 22 minutes 59.394 seconds
2. Nick Heidfeld (Ger) BMW Sauber 9.383 seconds behind
3. Lewis Hamilton* (GB) McLaren-Mercedes at 10.539secs
4. Fernando Alonso (Spa) Renault 14.478
5. Sebastian Vettel (Ger) Toro Rosso-Ferrari 14.576
6. Robert Kubica (Pol) BMW Sauber 15.037
7. Sebastien Bourdais (Fra) Toro Rosso-Ferrari 16.735
8. Mark Webber (Aus) Red Bull-Renault 42.776
9. Timo Glock** (Ger) Toyota 67.045, 10. Heikki Kovalainen (Fin) McLaren-Mercedes one lap behind
11. David Coulthard (GB) Red Bull-Renault one lap
12. Nico Rosberg (Ger) Williams one lap
13. Adrian Sutil (Ger) Force India-Ferrari one lap
14. Kazuki Nakajima (Jpn) Williams-Toyota one lap
15. Jenson Button (GB) Honda one lap
16. Jarno Trulli (Ita) Toyota one lap
17. Giancarlo Fisichella (Ita) Force India-Ferrari one lap
18R Kimi Raikkonen (Fin) Ferrari two laps
R Rubens Barrichello (Brz) Honda 19 laps completed
R Nelson Piquet (Brz) Renault 31 laps
Key: R = retired
Fastest lap: Raikkonen, 1:47.930, lap 24
* Hamilton penalised 25 seconds for gaining an advantage by cutting a chicane
** Glock penalised 25 seconds for ignoring yellow warning flags
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