With five games left, Leipzig are guaranteed to finish their first Bundesliga season in the top four.
The first three teams in Germany's top flight qualify directly for the Champions League, while the fourth-placed side goes into a play-off for a group stage berth.
Danish striker Yussuf Poulsen gave hosts RB an early lead before putting Werner in behind the Freiburg defence just before the break for his 16th league goal this season.
"It was another important step. Now we want to achieve more and fulfil our next dream," said Werner, with one eye on Europe.
This was Leipzig's fourth straight win and their Champions League chance is reward for a club that started their first Bundesliga season with a record 13-match unbeaten run.
"Of course, I am delighted," said coach Ralph Hasenhuettl. "We were prepared for a very hard game and we found the right solutions.
"We took the pace out of the game with the third goal and you could see in the second-half that Freiburg certainly know how to play.
"But once we went 3-0 up, we managed to calm the game down."
Leipzig are the only club from the former East Germany in the top tier.
There could be two German clubs making their Champions League debuts next season as third-placed Hoffenheim are also on course for a group stage berth alongside runaway league leaders Bayern Munich.
Saturday's win for Leipzig was over-shadowed by the death of a 56-year-old fan who collapsed before kick-off with heart failure and died later in hospital.
"Football now takes a backseat for us. Our condolences and deep sympathy are with the family of the deceased," the club wrote on their Twitter account.
It is the second time in recent weeks that an RB fan has passed away on the day of a Leipzig home game after a supporter also died before their defeat to Wolfsburg on March 11.