Centre-back Nicolas Lombaerts struck the post in the first half, while substitute Christian Benteke had a header cleared off the line by Gareth Bale at the death as Belgium were forced to share the spoils in their Group B encounter in Brussels.
Belgium - unbeaten after three matches - are four points adrift of group leaders Israel and three behind Wales in the race for the top two spots following Sunday's stalemate.
But Wilmots remained buoyant about Belgium's performance and their chances of qualification post-game.
"We did our best tonight – we shouldn't be upset," said Wilmots.
"We didn't quite do it tonight, but we can do it next time; five points out of nine it is not a catastrophe. Every team will get points.
"We played to win and we pushed them back. We tried everything, but to improve we have to take our chances. We hit a post and [Nacer] Chadli had a big chance.
"Belgium deserved to win – we had five or six chances but lacked the final touch. We will keep on working to get into the top two positions in the group."
