Team-mate Nico Rosberg, who was quickest earlier in the day, ensured another one-two for the German constructor as he finished 0.604seconds behind Hamilton, while defending champion Sebastian Vettel failed to set a time after his Red Bull underwent an engine change.
Championship leader Rosberg was first to benefit from his softer tyres as he broke the one minute 50secs barrier for the first time in the day.
However, his time at the top was short lived as Hamilton immediately went faster in a time of 1:49.189secs, which ensured he finished top of the standings.
Ferrari's Fernando Alonso was the only other driver to break the 1:50secs mark and finished third - the Spaniard escaping the issues experienced by team-mate Kimi Raikkonen at the rear of his car.
The Finn consistently aired his frustrations over team radio as he was only able to clock the 15th fastest time, over three seconds behind Hamilton.
Felipe Massa (1:50.327secs) was fourth in his Williams, while team-mate Valtteri Bottas was sixth as the Williams' sandwiched McLaren's Jenson Button.
Unlike his fellow Red Bull driver Vettel, Daniel Ricciardo was able to get his car out on the track but the Australian endured another frustrating session and could only finish eighth.
Daniil Kvyat was seventh, while Kevin Magnussen and Nico Hulkenberg completed the top 10.
Lotus' Pastor Maldonado, meanwhile, joined Vettel in not setting a time during the 90-minte session as he spun off on his first timed lap.