Goals from Carlos Tevez and Roberto Pereyra secured all three points, however it was Padoin – playing as a makeshift defensive midfielder – who earned the most praise from Allegri.
With Andrea Pirlo and Claudio Marchisio both unavailable due to injury, the 31-year-old was handed a new role and Allegri was delighted with his display.
"Padoin is proving himself to be a great professional," he told Sky Sport Italia. "He's tactically intelligent and it's tough to play in front of the defence.
"He brings balance to the side and anywhere you put him, he does the job.
"I am very happy with the performance, especially as it was Padoin’s first time playing in front of the defence.
"Empoli are a very organised side and played well, so we had to play between the lines and the only way to open them up was to keep moving their defenders from one side to the other.
"I'd say it's a great victory against a team in good shape who were unbeaten in eight games."
Juve's joy was only dampened by an injury to Arturo Vidal, however Allegri expects the Chilean – and Marchisio and Pirlo – to be available again soon.
He added: "Marchisio will be available against Fiorentina on Tuesday, while I hope to have Pirlo against Monaco, though he's been out for six weeks so we have to introduce him back slowly.
"Arturo Vidal [who went off injured] just had a knock to the ankle, it's nothing serious."
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