The Spaniard, who had shared the record of 33 Masters titles with the Serbian world number one, warmed up for the defence of his Roland Garros crown by securing his ninth Rome title.
Nadal got off to a flying start by whitewashing Djokovic in the opening set. It was the first time there has been a 6-0 set during a meeting between the two rivals.
Djokovic took the second by breaking Nadal's serve for the first time while leading 5-4, but the second seed responded in style by storming through the decisive set.
When Nadal's previous three claycourt tournaments had ended in semi-final defeats, it no doubt gave his rivals hope that his long reign at Roland Garros could be coming to an end this year.
However, the way he demolished the world's top ranked player in the opening and third sets on Sunday would have once again struck fear into any of those challengers who had been harbouring hopes of lifting the Musketeers' Cup on June 9.
The Spaniard heads into Roland Garros in top form after seeing his serve broken just twice en route to claiming his first title of 2019 in his 50th Masters final.
The 32-year-old left Djokovic in a daze as he stormed through the opening set in 39 blistering minutes.
The top seed fought back in the second as he saved four break points before winning the decisive game on Nadal's serve to take the set 6-4.
But the Serb, who had survived three-set battles against Argentines Juan Martin del Potro and Diego Schwartzman to reach the final, faded in the final set as he dropped his opening service game before Nadal surged clear.
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