Williams began to show their expected speed with Felipe Massa fourth and Valtteri Bottas sixth, sandwiching the McLaren of Jenson Button. The British squad are likely to enjoy more long-run pace than Alonso come Sunday's race, putting them in strong contention for a podium.
Elsewhere, Sebastian Vettel sat the entire session out after suffering engine problems during FP1. The two-time Belgian winner is now marginal on units for the season.
The session was cut short by a pair of red flags. First Pastor Maldonado suffered a sizeable shunt, running wide and then spinning into the barriers on the approach to Pouhon, ending his session after less than 10 minutes.
The second came thanks to Esteban Gutierrez, who spun and stalled with what was later reported to be an energy recovery system (ERS) issue. The Mexican sat out FP1 while reserve driver Giedo van der Garde took the controls, meaning he has completed just seven laps thus far in Belgium.