Atalanta’s wonderful performance over the two legs ensured the Italian side reached the semifinals of the Europa League on a 3-1 aggregate scoreline.
The final of the Europa League will be in Dublin on May 22.
Liverpool substitute, Conor Bradley, scored an own goal just after the break.
The 120-times capped Bonucci was part of Italy’s Euro 2020-winning team and is a nine-time Serie A champion.
Errors by United goalkeeper David De Gea and defender Harry Maguire gave the home side an early goal.
The England international has been in fine form for Erik ten Hag’s side in recent months.
Barcelona left it late to edge Manchester United to an interesting 2-2 draw in the first leg of the UEFA Europa League playoff at the Camp Nou Thursday evening
The first leg matches of the ties are scheduled for February 16, with the second leg matches a week later on February 23.
“We will have to compete, going to Manchester against a really tough rival,” Xavi said ahead of Tuesday’s trip to Osasuna in La Liga.
Manchester United defeated Sheriff 3-0 to keep the hope of top place finish alive.