Ter Stegen was unexpectedly named in the team for the Copa del Rey clash against Guadalajara on Tuesday, his first competitive appearance in months following a lengthy injury layoff.
The decision came as a shock, with many anticipating that Wojciech Szczesny would deputise for the rested first-choice keeper, Joan Garcia.
However, Flick opted for his German compatriot, a move that paid dividends in a 2-0 victory, taking them to the next round.
Flick speaks on Ter Stegen's return
Speaking after the match, Flick explained that the decision to start Ter Stegen was a deliberate one made by the entire coaching staff to honour the goalkeeper's long-standing service to the club.
"Marc is the captain and has played many games in the 12 years he has been here," Flick stated, as reported by Goal.
"We talked with the rest of the coaches and we wanted to give him the opportunity to play. He is back, it is only for this match and I think it is a good next step."
The manager stressed that the start was a reward for Ter Stegen's dedication during his recovery, where he has supported the team while Garcia established himself as the new number one.
"He is the team captain," Flick added. "He had the opportunity to return and he took it. He has given a lot to the club and must be respected."
Despite the glowing praise, Flick was quick to manage expectations and reaffirm the current goalkeeping hierarchy.
"We discussed it with the staff and we considered that he should play," Flick reiterated, before adding a crucial clarification: "It is just for this match."
For Ter Stegen, the night marked a significant personal achievement. After a gruelling rehabilitation, returning to the pitch with the captain's armband and contributing to a win was the perfect comeback.