Nadal apologises to Wimbledon opponent after testy exchange
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Second seed Nadal, the champion in 2008 and 2010, reached the fourth round for the 10th time with a 6-1, 6-2, 6-4 win.
The 36-year-old had required back-to-back four-setters to make the third round and was expected to be tested by Sonego, who made the fourth round last year.
However, Nadal did not face a break point until he dropped serve in the eighth game of the third set, his focus possibly affected by a stoppage to close the Centre Court roof.
He quickly broke back and sealed the victory.
Nadal, however, appeared upset by the noise the Italian was making on court.
He even summoned Sonego to the net to discuss his displeasure while the two then had another lengthy exchange as they shook hands.
"It's something that I spoke with him in the locker room and it stays there. Only thing I can say is I saw him personally.
"My intention was never to bother him at all. Just to tell one thing that was bothering me that I think he was doing in that moment, but that's it.
"We had some issues there, but that's it."
Nadal has already won the Australian Open and French Open in 2022 and is halfway to the first men's calendar Grand Slam since Rod Laver achieved the feat in 1969.
"This was probably my best match here without a doubt during the championships, against the most difficult player I faced," Nadal said.
"I have been able to raise my level, super happy for that."
Nadal will next face Dutch 21st seed Botic van de Zandschulp for a place in the quarter-finals.
The 26-year-old Van de Zandschulp made the last 16 at the All England Club for the first time with a 7-5, 2-6, 7-6 (9/7), 6-1 win over French veteran Richard Gasquet.
Nadal comfortably defeated the Dutch player in straight sets on his way to a 14th French Open title last month.