Valtteri Bottas threw his name into the mix for a shot at pole position for Sunday's Belgian Grand Prix after topping the timesheet in final practice.
Early morning rain that eventually relented two hours from the start of the final session ensured it was a damp start on the Spa-Francorchamps track once FP3 commenced in very cool 13 degrees conditions.
Installation laps were conducted either on full-wet or intermediate tyres, and with only three drivers setting a time in the opening 30 minutes as teams waited for the circuit to dry out.
Sauber's Esteban Gutierrez was eventually the first to venture out on slick rubber, with the Mexican posting a time just over one minute 56 seconds.
That was seven seconds off of Hamilton's best on Friday, highlighting the fact there was more to come from the track providing further rain stayed away.
It was not until with 18 minutes remaining the session finally became busy, with all drivers on the circuit on the medium-compound Pirelli tyres.
Come the final five minutes and the switch to the quicker softer tyre it was Williams' Bottas who prevailed with a lap of 1:49.465secs.
That, however, was still three tenths of a second slower than Hamilton's eye-catching time on Friday.
As for the title-chasing Briton, the 29-year-old was forced to settle for a relatively lowly - by Mercedes' high standards - fifth fastest.
Hamilton finished 0.352secs down on Bottas, setting exactly the same time as Ferrari's Kimi Raikkonen, whose lap was posted earlier so he had the honour of being fourth on the timesheet.
Nico Rosberg, 11 points clear of Hamilton in the drivers' standings with eight races to run, was third, 0.078secs clear of his main title challenger.
Red Bull's Daniel Ricciardo, the only driver other than Rosberg and Hamilton to win a race this season, was second quickest, a quarter of a second adrift of Bottas.
Ferrari's Fernando Alonso and Daniil Kvyat in his Toro Rosso also set lap times in the one minute 49s, with McLaren's Jenson Button, Felipe Massa in his Williams and the second Toro Rosso of Jean-Eric Vergne completing the top 10.
Reigning four-times champion Sebastian Vettel, who sat out the entire second session on Friday due to a power-unit change, encountered more problems in FP3.
On this occasion a section of brake-duct cover broke off and lodged in the duct itself, leaving the Red Bull covered in tape when it re-emerged, and the German down in 13th come the conclusion of the hour-long session.
Marussia's Max Chilton was 20th, nearly half a second behind team-mate Jules Bianchi, but at least ahead of Caterham duo Marcus Ericsson and debutante Andre Lotterer.