Clarke took his tally for the season to 12 goals when he collected a pass from Mat Sadler on the edge of the box, turned and curled a superb shot over goalkeeper Jamie Jones and into the roof of the net after 11 minutes.
"It was a bit of magic from Billy Clarke," said Williams, who thought Town were worthy winners in east London.
"I was sitting in the dug-out and thought it was a bad cross but it ended up in the back of the net, although he assures me it was meant.
"But the lads deserved the win, it was pretty much a good team performance and they worked hard for each other. We created chances in both halves and could have been out of sight but in the end, we were hanging on.
"It was a lively pitch and not easy to pass the ball around and play football and we had to ground it out. But the pleasing thing was that we also kept a clean sheet.
"The way we played last Monday (in a 1-1 home draw with Doncaster) and here today, I think it shows that we are getting the rewards for what we are asking of the team.
"As I said, we could have put the game to bed. But that always happens when you are only winning by the one goal - you are always vulnerable to conceding. However, in the last five minutes the lads were putting their bodies on the line.
"Overall, I think it was a good solid team performance and I think we did very, very well."