Neuer, who was born in Gelsenkirchen and grew up watching from the terraces at the club's former Park Stadion, made a controversial switch to the Bavarians in the summer.
He returns to the Arena for the first time this weekend and Howedes hopes he is given the reception he deserves, even though he knows it is unlikely.
"I think he is going to have to expect some whistles and he knows that, but I still believe that Manuel does not deserve any animosity," he told Kicker magazine.
"He always performed really well, if not sensationally for us."
And Howedes does not expect his side to gain any advantage if the fans do jeer Neuer each time he touches the ball.
"Manuel will not lose his concentration," he predicted. "He has always made great saves when he is under particular pressure."
Dortmund, meanwhile, are not in action until Sunday when they travel to Hannover.
Lukas Podolski inspired Cologne to a 4-1 win over Bayer Leverkusen in Stale Solbakken and Robin Dutt's first Rhineland derby in charge of the respective local rivals.
Borussia Monchengladbach climbed to second in the standings with a narrow 1-0 victory at rock-bottom Hamburg.
Nurnberg fought back to secure a hard-fought 1-1 draw in horrendous conditions against 10-man Werder Bremen.
Hoffenheim kept up the pressure on the leaders as two goals from Roberto Firmino guided them to a 3-1 victory over Wolfsburg.
Kaiserslautern came from behind to win their first Bundesliga match of the season, beating local rivals Mainz 3-1 at the Betzenberg.
Augsburg survived the late dismissal of Sebastien Langkamp to hold on for an decent 2-2 draw on the road at Hertha Berlin.
Martin Harnik scored twice as Stuttgart gained a 2-1 victory at Freiburg.
In Friday's only game, Stuttgart edged closer to the Bundesliga summit with a 2-1 win over Freiburg.