The 30-year-old, who only made 10 Bundesliga appearances in 2017/18 due to a persistent back complaint, started for Dieter Hecking's side as he continues to make his way back to form and fitness, having featured in the second half of Gladbach's 2-0 friendly victory over VfB Lübeck on Friday.
Johnson could have scored within seconds of kick-off against Flensburg, only to see his shot from a tight angle saved. He did find the net moments later, however, latching onto Oscar Wendt's ball down the left to slot in the opener in the fifth minute.
The 57-time USMNT attacker doubled his tally in the 13th minute, superbly controlling a ball from Christoph Kramer on his chest, before flicking it around the goalkeeper and tapping into an empty net. Torben Müsel made it 3-0 after just 22 minutes as Gladbach overpowered their lower league opponents, with Brazilian attacker Raffael adding a fourth in what was ultimately a comfortable win.
The game came too soon for new signing Alassane Plea to feature, while several other Gladbach stars, including Thorgan Hazard, Yann Sommer and Matthias Ginter, were also absent due to their involvement in the World Cup.
Watch: 60 Seconds Under Pressure with Johnson
Gladbach get their Bundesliga season under way at home to Bayer Leverkusen on Saturday 25 August.