Thorgan Hazard -- the younger brother of Chelsea midfielder Eden -- gave Gladbach a shock, yet deserved first-half lead.
But goals in the final 25 minutes, from Arda Turan and Gerard Pique, sealed Barcelona's second Group C win after their 7-0 hammering of Celtic at the Camp Nou a fortnight ago.
With Messi out due to a groin injury, Barca coach Luis Enrique opted to start Spain international Paco Alcacer in the superstar's place alongside Neymar and Luis Suarez.
Neymar and Suarez were rarely allowed more than a split-second on the ball.
Gladbach had the better of the opening exchanges at Borussia Park and fulley merited their lead.
Referee Damir Skomina missed a handball in the area when the ball clipped Gerard Pique's arm from Hazard's cross in the first five minutes, but then Gladbach took the lead with their first dangerous attack.
Raffael dispossessed Sergio Busquets and broke into the Barca half before feeding Mahmoud Dahoud, who timed his pass into the box perfectly, flicking the ball into Hazard's path.
It was clearly not the homecoming ter Stegen had envisaged, having left Gladbach in 2014 for Barca after 18 years with the Bundesliga club.
Gladbach managed to disrupt Barcelona's game until just after the hour mark.
Germany midfielder Christoph Kramer was subduing Neymar while Dahoud was the creative spark in midfield.
Turan came on for Ivan Rakitic on the hour mark and it proved to be an inspired switch as he scored five minutes later.
Neymar finally shook off Kramer to float a pass over the top of the Gladbach defence.
The winning goal came just nine minutes later.
Neymar's corner was deflected into the path of Suarez, who was unmarked in the area.
He slammed in a powerful shot, which was blocked by Sommer, but Pique was on hand to tap home the loose ball from close range, to Enrique's delight.
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