The result leaves the Latics second in Group D with four points from their opening two games, but Watson stressed that their league form is the most important thing.
"It was our first European victory and we deserved the win," Watson told BT Sport after the match.
"Our main aim is to get back into the Premier League - we've got a fantastic squad. First and foremost is the league form."
Watson also reserved special praise for goalkeeper Scott Carson after his performance.
"Scott Carson made a great save, he was brilliant," he added.
Wigan are currently 15th in the Championship having picked up 11 points from their opening eight games.