Luis Suarez put the hosts up 1-0 in the 29th minute with an assist from Messi, who doubled the lead four minutes later with a goal of his own and went on to set up Antoine Griezmann”s marker in the 67th minute.
Dortmund enjoyed an edge in possession, yet the best they could do was a consolation goal by Jadon Sanchez with 13 minutes left in regulation.
Despite the loss, Dortmund remain in the fight for second place in Group F, tied on points at 7 with Inter Milan, who prevailed 3-1 Wednesday against Slavia Prague.
Chelsea and Valencia are tied on points at 8. The Blues will host Lille at Stamford Bridge on Match Day 6.