Leipzig Celebrates Qualification
Leipzig smashed in three quickfire second-half goals in Warsaw to secure second place behind Real Madrid in Group F and crush the Ukrainian club's dreams of a fairytale berth in the last 16.
"I'm really proud of the team. We didn't start well in this Champions League campaign, but we put in a solid performance today and are really happy to be through," forward Emil Forsberg told DAZN.
There was a bittersweet note to Leipzig's success, however, after Werner was substituted off early in a potential blow to his World Cup hopes.
The former Chelsea forward was replaced by Forsberg after picking up a knock to his ankle in a clash with Shakhtar captain Taras Stepanenko.
Leipzig started more brightly than their opponents and were rewarded with an early goal, Christopher Nkunku pouncing on the rebound after Werner had forced a save from Anatoliy Trubin.
Shakhtar's hopes of launching a comeback were dashed when Andre Silva bundled in a second from close range just after halftime.
The Ukrainian side thought they had a penalty a few minutes later after a tackle on Lassina Traore, but VAR showed the Burkinabe had drifted offside earlier in the move.
Dominik Szoboszlai rounded Trubin to slide the ball in for Leipzig's third just after the hour mark before Dani Olmo came off the bench to help complete the rout.
The Spain international curled the ball in off the post just seconds after taking to the field, though the goal was later ruled to be an own goal due to a deflection off Valeriy Bondar.
Leipzig join fellow Bundesliga clubs Bayern Munich, Borussia Dortmund and Eintracht Frankfurt in the last 16.
Shakhtar, meanwhile, drop down to the Europa League after finishing third in Group F.