Two-time world champion Pogacar joined Jacques Anquetil, Eddy Merckx, Bernard Hinault and Miguel Indurain as the most successful riders in Tour history.
Pogacar had all but secured his historic title during the previous two mountain stages that finished on the iconic Alpe d’Huez climb.
The 27-year-old Slovenian won five stages and had been in yellow since his victory in the Pyrenean sixth stage.
He now has 26 stage victories in total, putting him fourth in the all-time list behind only Mark Cavendish (35), Merckx (34) and Hinault (28).
He also surpassed both Indurain and Chris Froome for total days spent in yellow with 70, and trails now only Hinault (75) and Merckx (96).
He is the youngest rider to have won five Tours, more than a year younger than Merckx was in achieving the same feat, and is the first person to finish on the podium seven years running.
He is also the only rider to have been on the podium in nine consecutive Grand Tours.
And the Slovenian played his part in a stunning final stage, which was shortened to 88.7km due to wildfires raging in the southwest.
Van der Poel and Pogacar escaped together on the final climb up Montmartre with 10km to ride and then fought to the finish with a chasing group of sprinters closing in.
As Pogacar’s strength sapped inside the last 700 metres, and with the chasers just seconds behind, Van der Poel struck out alone.
The cobbled classics specialist held on to win by half a wheel length in a photo finish from his Alpecin Premier Tech team-mate Jasper Philipsen, with Mads Pedersen in third.