Mertesacker, who had been out since February after ankle surgery cut his club season with Arsenal short and returned to action only a few weeks ago, collided with Jerome Boateng in training on Thursday.
"There was a bit a of a doubt about him yesterday after he collided with Jerome Boateng during a corner. He was lying on the ground but it turned out to be less dramatic," Flick told reporters just before the team's flight to Lviv, Ukraine.
"We now have all players fit and ready to play in our match tomorrow," he added.
Mertesacker is likely to feature in a central defensive partnership with Holger Badstuber, while captain Philipp Lahm has been switched from right back to left back.
It is not yet clear who will play in Lahm's usual position with Boateng and Lars Bender battling for that starting spot.
"The final decision on that will be taken after this evening's final training in Lviv," said Flick.
He said coach Joachim Loew won't announce the starting team to the players until a few hours before the game to keep them on edge.
"We have our line-up in our heads. There is some uncertainty (among the players) whether they will play or not. That is good because it keeps the concentration high right until the end."
Among those waiting to find out if they will start are forwards Miroslav Klose and Mario Gomez, with the former looking to have the edge despite the Bayern Munich forward's prolific season as second-top scorer in the Bundesliga with 26 goals.
"Both are top quality strikers and each has their own personal strengths," said Flick. "The last two years Mario has had an impressive goal quota."
"It is a tight race and Miro has not had a lot of matches (due to a five-week injury break) but he has shown us here that he is ready," Flick said.