Last night’s defeat leaves Scotland fourth in Group I, level on points with Kazakhstan but trailing the Belgians by six points and Russia by three.
The latter two nations visit Hampden in September as Scotland seek to get their Euro 2020 qualifying campaign back on track.
Belgium away was always going to be the toughest game, and so it proved with two goals from Romelu Lukaku and a late third from Kevin De Bruyne clinching the win for the No 1 ranked side in the world.
Clarke, who oversaw a narrow home win over Cyrpus on Saturday in his first game in charge, praised Scotland for their commitment and tactical nous and noted that Lukaku looked offside when he tucked home his second.
“It was difficult game for us,” the national coach admitted. “I don’t think we deserved the third goal at the end and I could say the second goal was offside, which could have changed things. My overall impression is that I have a good group of players who are committed to their country.
“They were competitive in the game against the No 1 team in the world. We have shown in the work done in this 10-day camp, but we need improvements. We need to be better on the ball, but we have grown as a group. We need to be ready to go again against two good sides again in the autumn.” Scotland host Russia and Belgium at Hampden on 6 and 9 September, respectively.