The German had opened the scoring for the Premier League Champions before substitute Manor Solomon levelled for the visitors 12 minutes later to salvage a point.
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“Unfortunately, we just got a draw,” he said. “We have to accept it but we are through as group leaders and that’s the most important thing.
“There’s still a lot to improve. We knew the game would be tough.
“We let Shakhtar do a great job – we let them play and we didn’t defend as well as we normally do.
“The build-up was a bit slow and we struggled to create. Unfortunately, it was not our best performance, but this is the Champions League.
“It’s a competition where you need to struggle for the future. You have to learn from it.
“Then, when the knock-out stages start, we will be prepared for it.”
Although he was disappointed not to have netted the winning goal, the German thanked his teammates for their creative efforts.
“Obviously, I wanted the goal to be the decisive goal which won the game,” he admitted.
“Gabby kept the ball and then saw me. It wasn’t difficult for me to score.”
Despite the draw, Gundogan added he feels the squad will be in good shape for the knock-out stages, as City look to conquer all competitions.
“We are on the way,” he declared. “In the Premier League, we are nine points behind the leaders – it’s not what we aimed for but this is the situation you have to deal with.
“The Premier League is so competitive and strong. We dropped unnecessary points in some games. To be able to maintain your place at the top, you’re not allowed to.
“Liverpool are impressing week by week but we need to be there if they make a mistake to close the gap.
“In the Champions League, we are through as leaders – that’s the most important thing.
“There is still plenty of room to improve – not the results because I think they will come automatically – but the way we play offensively and defensively.”