The 25-year-old was given a huge reception when his name was announced in Jurgen Klopp’s injury-stricken side before kick-off, and he responded by helping set up the first for Adrian Ramos and scoring the second at Signal Iduna Park.
Kagawa, who scored just six goals in 38 Premier League appearance for Manchester United, has now managed 22 in 50 Bundesliga outings for Dortmund.
Substitute Pierre-Emerick Aubameyang sealed the victory with a sumptuous dink over goalkeeper Roman Burki in the 78th minute, with Oliver Sorg's last-minute effort scan consolation for the visitors.
It was Dortmund’s ninth successive win over Freiburg, during which time they have scored 29 times and conceded just four.
The result elevated Jurgen Klopp’s men to third in the Bundesliga, one point behind pacesetters Bayer Leverkusen and Bayern Munich.
Freiburg, meanwhile, have taken just one point from a possible nine - and a repeat of last season's top-half exploits looks unlikely.
Talismanic attacker Marco Reus recently joined Mats Hummels, Ilkay Gundogan and Nuri Sahin on the Dortmund treatment table, with Klopp bringing in Kagawa and electing to start Adrian Ramos in place of Aubameyang at the spearhead.
It was the visitors who had the first chance. Admir Mehmedi raced in behind the Dortmund backline and into the area, but Roman Weidenfeller repelled the Switzerland forward's firm strike.
It was then the Freiburg goalkeeper's turn to preserve the deadlock. Milos Jojic turned cleverly and sent Kevin Grosskreutz through on goal, but his first-time effort was deflected wide by the legs of Roman Burki and Marc-Oliver Kempf had to be alert to turn the winger's ball for Kagawa behind.
Dortmund made the breakthrough they deserved after 33 minutes, and it was indebted to Kagawa.
The 25-year-old Japan international spun his man delightfully and pierced open the Freiburg defence with a throughball into Grosskreutz who cut the ball across goal for Ramos to stab his second league goal for Dortmund home.
In the 41st minute, Signal Iduna Park erupted as its returning hero made it 2-0.
Following a neat passing move, Ramos crossed from the right and after Henrikh Mkhitaryan had failed to connect with an attempted shot, Kagawa accurately buried the ball in the bottom corner from just inside the area.
The second half began at a much slower pace. Just after the hour, Kagawa went down with suspected cramp and hobbled off to a standing ovation.
Ciro Immobile came on in his place and almost made an immediate impact. The Italy striker shrugged off one challenge, and cleverly cut inside Kempf, only to fire straight into the arms of Burki.
But another substitute did get Dortmund's third. Aubameyang's electric pace got him beyond the Freiburg defence and though Burki rushed from his line, the Gabon forward clipped it over him and into the back of the net.
There was some consolation for Freiburg, though, as Oliver Sorg scored their first goal of the season late on to ensure it finished 3-1 to Dortmund.