Valtteri Bottas completed a sweep of Portuguese Grand Prix practice on Saturday adding to his success at Friday's practice session.
The Finn, quickest in both Friday's sessions at the Algarve circuit near the southern city of Portimao, lapped with a best effort of one minute 16.654 seconds.
Hamilton, the six-time world champion who can take an outright record 92nd career win on Sunday after equalling Michael Schumacher's milestone, was 0.026 slower on a sunny but cool morning.
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Both drivers made errors, with Hamilton tracking through the gravel at one point.
Red Bull's Max Verstappen was third fastest, 0.158 off the pace, with AlphaTauri's Pierre Gasly - whose car caught fire on Friday - fourth on the timesheets.
The session was ended a minute early after a drain cover came loose at the exit of turn 14 as Sebastian Vettel's Ferrari went over it.
Mercedes have qualified on pole for every race so far this season and look set to extend that run to 12 in a row later on Saturday.
The team can also clinch a record seventh successive constructors' title on Sunday if results go their way, although Red Bull's form is likely to keep them waiting at least another week.
Hamilton is 69 points clear of Bottas after 11 races.
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