The young Australian and Samsonova were involved in a titanic struggle on Grandstand court before the Russian triumphed 7-5 6-7 (6-3) 6-2.
Joint went toe-to-toe with the world No.55 and made her work for almost three hours in hot and humid conditions.
It was always going to be a tough encounter between two players high on confidence after their morale-boosting second-round wins in a WTA-1000 tournament.
Joint came into the last-32 contest fresh from eliminating world No.18 and 14th seed Sorana Cirstea in straight sets, while Samsonova bundled out world No.26 and No.22 seed Barbora Krejcikova.
The Russian seized the initiative by taking the first set, but only after Joint gave her much to think about after clawing her way back from 5-1 down.
In the second, the 20-year-old showed maturity beyond her years to hold her nerve and prevail in a tiebreaker to level the match.
They each held serve at 2-2 in the deciding set before the 27-year-old Samsonova, making full advantage of her top-spin forehand and moving her younger opponent around the court, earned a vital break in the fifth.
It proved pivotal as Samsonova added more heat by holding serve and breaking Joint again to complete a tough win.
Also in the round of 32, Canadian Leylah Fernandez took full advantage of her local support by destroying No.5 seed Mirra Andreeva in straight sets.
Fernandez beat the world No.5 Andreeva 6-1 6-4 to send the reigning French Open champion packing in an hour and 20 minutes.
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