Ikay Gundogan gave Dortmund the lead from the penalty spot before an Adrian Ramos brace either side of Shinji Kagawa’s strike handed Thomas Tuchel’s men the win.
Dortmund are currently second in the Bundesliga table, while Eintracht sit a lowly 14th at the seasonal break.
The Borussia outfit next play South Korea’s Jeonbuk Hyundai Motors FC at Al Wasl Sports Club on Friday.