Lewandowski made his announcement to the squad in the dressing room before Flick faced the press ahead of the penultimate La Liga fixture. The striker departs after four seasons in Catalonia in which he won three La Liga titles, one Copa del Rey and three Spanish Super Cups.
Flick, who has worked with Lewandowski across both his Bayern Munich and Barcelona tenures, made no attempt to disguise the personal significance of the departure.
"The conversation went well. He spoke to the squad and said his goodbyes. It's been a great chapter for him and he made that very clear. For me, it's been a privilege to work with him because he's a true professional. He's a role model, which is why he's still performing at this level. Now he wants a new challenge, and we respect that."
He was direct about the difficulty of finding a comparable replacement.
"It's clear that it won't be easy to find someone of Robert's level. He's a spectacular professional and a great person. We'll miss him, but we have to restructure. We have time to look at the market."
Flick also confirmed that Frenkie de Jong will miss Sunday's match through illness and that Marcus Rashford remains a doubt. The Englishman will not start but could be named in the squad. Andreas Christensen is expected to feature for a few minutes from the bench, as is goalkeeper Joan García, who will start ahead of Wojciech Szczęsny regardless of the Zamora Trophy implications.
Barcelona can make history on Sunday by becoming the first La Liga side to win all 19 home matches in a 38-game season.