"In the first half we played very well against well-organised opponents. I had to make that clear to my team at half-time because they were feeling a bit negative.
"By the end we were happy because these were important points in the relegation battle."
Labbadia started Czech Republic midfielder Vladimir Darida in the only change from last Saturday's win at Hoffenheim in his first home match in charge.
Union's Urs Fischer, who guided the east Berlin outfit to the top-flight for the first time this season, brought in four fresh faces to his starting lineup after Sunday's loss to champions Bayern Munich.