Hegseth's announcement in a social media post followed remarks by Trump who appeared to play down the incident near the musician's house in Nashville, Tennessee.
"They probably shouldn't have been doing it. But they like Kid Rock. I like Kid Rock," Trump said on Tuesday.
"Maybe they were trying to defend him."
Reuters, citing a US official, reported earlier on Tuesday that aircrew involved in the incident had been suspended after appearing to deviate from their mission.
The US military is supposed to be apolitical, loyal to the US Constitution and independent of any party or political movement.
Rock posted a video on X on Saturday, standing in front of his swimming pool and saluting one of the helicopters.
Hegseth, who has a home in Tennessee, praised Kid Rock as he exonerated the crew.
"Thank you @KidRock. @USArmy pilots suspension LIFTED. No punishment. No investigation. Carry on, patriots," Hegseth wrote on X.
Military helicopters were also seen flying close to demonstrators in Nashville taking part in organised protests against Trump's policies that were part of the anti-Trump "No Kings" rallies that took place across the country.
Reuters reported on Monday that the army was investigating the incident and an Army spokesman declined further comment when contacted by Reuters on Tuesday.
"Army aviators must adhere to strict safety standards, professionalism, and established flight regulations. An administrative review is underway to assess the mission and verify compliance with regulations and airspace requirements," US Army spokesperson Major Montrell Russell said on Monday.
"Appropriate action will be taken if any violations are found. Until the review is complete, there will be no further comment," Russell added.
Since being sworn in last year, Hegseth has moved quickly to reshape the military, firing top generals and admirals as he seeks to implement Trump's national security agenda and root out diversity initiatives he calls discriminatory.
Democratic lawmakers have warned the Trump administration is increasingly trying to use the military for political gain.
In his post about the helicopters, Rock took a swipe at Democratic California Governor Gavin Newsom, adding: "God Bless America and all those who have made the ultimate sacrifice to defend her."
