Luis Muriel was also on target for the Friuliani, with Eder having cancelled out Di Natale's opener.
The result puts Udinese sixth, with Samp 15th.
The Friulani had won four in a row to get back into the European places and aimed to continue their eight-month unbeaten home run in Serie A.
Samp were starting to feel the heat after failing to win in seven, as they were only six points clear of the drop zone. The defence was completely revamped, as Daniele Gastaldello and Angelo Palombo were suspended with Andrea Costa and Nenad Krsticic injured.
There was an early scare after five minutes when Sergio Romero dropped a cross, but Antonio Di Natale was not expecting it and couldn’t take advantage.
Udinese broke the deadlock with a classic Di Natale finish, as he gathered with his back to goal, spun round and immediately placed the angled drive into the far bottom corner past Romero’s fingertips.
However, Sampdoria drew level when Eder smashed a powerful curler into the far corner from outside the box, perhaps with a slight deflection to take it past Brkic.
After the restart Di Natale restored Udinese’s advantage with another sensational goal. He ran on to a long ball and waited for the goalkeeper to rush off his line, hitting on the volley so the ball looped over Romero to go in off the underside of the bar.
Muriel finished off the game with a sharp angled drive from 12 yards after Romero’s dreadful kick was straight at him.
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