Lukaku was the driving force from the start, imposing himself on the game and disrupting the Leverkusen defence to keep Inter in the hunt for its first trophy in nine years.
The quarterfinal lineup for the Europa League is set after Sevilla, Wolves, Bayer Leverkusen and Basel secured a place in the final-eight.
Prior to the game, the players had warmed up in t-shirts with '#BlackLivesMatter' written along with the slogan of the club's official "Reds Against Racism" campaign.
Kai Havertz became the first player in Bundesliga history to score 35 goals before turning 21 to help Bayer Leverkusen beat Freiburg 1-0.
The Bundesliga faces its next test this week as players return to live at home ahead of the weekend's games. Teams spent the seven days leading up to their first games in a group quarantine in hotels, but that was a one-off.
Kevin Volland bagged a brace while Leon Bailey and Lars Bender scored one each to help Leverkusen beat Dortmund 4-3.
Juventus were already assured of topping Group D and seemed sluggish at times in Germany, before Ronaldo scored from close range off substitute Paulo Dybala's cross in the 75th minute.
Bayer Leverkusen edged past Bayern Munich in a thrilling 2-1 win on Saturday, while a 10-man Dortmund side held on to their lead against Hertha Berlin.
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