The 30-year-old limped off midway through the second half and had to watch from the sidelines as the Championship side mounted a stirring comeback.
Reading were eventually undone by a goalkeeping error from Adam Federici in the first half of extra time as Alexis Sanchez's shot slipped from his grasp.
But after being knocked out of the Champions League to Monaco, Mertesacker is delighted with the response from his team-mates and making their second consecutive final appearance.
He said: “I twisted my ankle but obviously I am delighted that we are back at Wembley - that is a fantastic achievement for this group for the second consecutive time.
“We are really proud.
“It was a really tough game and we knew before that they would fight for their lives and give absolutely everything to keep us away from their goal and they did it fantastically. We are just delighted that we made it again.
“It is a little progress [and] it would be a great honour, back to back FA Cup wins. We were knocked out of the Champions League and that was a big blow for us but after that we responded and it is a great achievement. Let’s continue our great run.
“We just wanted to win and do something fantastic for the team and the group. You can see everyone is absolutely happy and delighted.”