Lewandowski has scored a remarkable 39 Bundesliga goals in 27 matches this season, putting him just one behind the record held by Gerd Muller, who netted 40 times in the league during the 1971-1972 campaign.
There were fears Lewandowski, who recently returned from a month out with a knee injury suffered while on international duty with Poland, could miss the clash with Freiburg after he made an early exit from a session at the club's training camp on Friday (AEST).
But Flick revealed the striker is ready to go after playing a part in the session and said helping him to the milestone is one of his last remaining targets before he leaves the club.
"Lewy took part in the training and is available," Bayern coach Flick said, with Freiburg and then Augsburg the final opponents for Bayern this season after Lewandowski scored a hat-trick in a 6-0 win over Borussia Monchengladbach last time out.
"The focus is on finishing the season well. We can reach 80 points – that's our goal.
"Lewy's 40 goals are next. If we can do both, that would be incredible and we will do everything to achieve it.
"If we can achieve both, it would be an outstanding thing, but to do that we have to deliver top performances twice.
"If the team implements what we set out to do, then Lewy will also benefit from it. You saw against Gladbach that the players are looking for him and support him.
"Lewy has also assisted a goal, so it's about giving and taking."
Alexander Nubel, who has been linked with a loan move to Monaco at the end of the season, is poised to start in goal for the first time in the Bundesliga this season as Manuel Neuer is rested.
Flick was also asked whether he believes Thomas Muller will be handed a Germany recall to play in UEFA Euro 2020 after producing 11 league goals and 17 assists in a fine season for Bayern.
"I don't know any more than you do," he said. "Thomas has been showing top performances for two years.
"It is more fun than a headache [for Germany]. You like to have a player like that in the team, he always gives everything for the team.
"We are glad that he performs so well so often. He always has to play in this team.
"But it is not my place to decide. This is a decision for Jogi [Germany head coach Joachim Low] and the coaching team, they will make the right decision."
Bayern has only lost one of ist past 35 Bundesliga games against Freiburg, though that was – like this upcoming clash – on Matchday 33 back in 2015.
Since a 0-0 draw with RB Leipzig in May 2019, Bayern has scored in each of its past 33 Bundesliga away games to equal the top-flight record it set between 2012 and 2014.