City only need a draw in Germany on Wednesday night to progress to the semifinals after a 2-1 win in the first leg at the Etihad Stadium.
Gundogan is aware of the atmosphere that can be created in the 81,000-capacity Signal Iduna Park but without supporters in attendance because of coronavirus protocols, the midfielder says his former club are at a disadvantage.
"First of all it changes the atmosphere," Gundogan told a news conference on Tuesday.
"There is not really a connection between fans and players and in the games that can be quite important. When you may face difficult periods in a game a crowd is always able to give you another push and lift you in a bad moment.
"Going to Dortmund, facing Borussia Dortmund knowing that there is no crowd feels like it's a bit of a disadvantage for Borussia Dortmund because I played there five years and I know how incredible the crowd is and the support is and how loud it can be also in that stadium."
City are looking to qualify for the semifinals of the Champions League for the first since 2016 when Manuel Pellegrini's side were knocked out by Real Madrid.
Under Guardiola's watch there have been shock exits to Monaco, Tottenham and Lyon and Gundogan insists that to avoid another against Dortmund, City will have to learn how to "struggle" when things are not going their way.
"Maybe it is something we are not used to, going behind and conceding or struggling because we are used to dominating games always and having possession but it is completely normal in the Champions League," he said.
"There are games that it might not be that easy and that are fluent on the pitch. Mistakes are normal so just learning to deal with it is the only thing that was a little bit missing."
City head into the game on the back of a surprise 2-1 defeat to 10-man Leeds United on Saturday.
The result is unlikely to make much difference in the Premier League title race and Gundogan says the setback may have been well-timed, coming ahead of games in the Champions League, FA Cup and Carabao Cup this month.
"Maybe it was a warning or a signal for us," he said.
"If it turns out to be like that. We will probably know after the game tomorrow. I'll take that defeat then.
"For us, the best case is always going into the game with the feeling we want to win that game. Defending results I don't feel like it fits us the way we are as players and the way we play generally as a team so we should try to go every single game to win the game. That's what we are used to."