Williams sealed the Lions' place in the Football League Trophy Southern final when he scored the second at Roots Hall.
However, Harris admitted that Millwall looked rusty in the opening minutes.
He is quoted by the club's official Twitter feed as saying: "They started the game as I expected after 10 days without a game while we had a tough run. I questioned the players for the first time on Saturday and asked for a response. What they did tonight was just that.
"On the whole I think we deserved to win the game. They were two quality goals. Our hold-up play and the way we linked things together was brilliant.
"Shaun Williams exemplified everything we did which was good tonight. He deserved that goal."
Millwall were knocked out of the FA Cup second round by Wycombe Wanderers on Saturday.