The two clubs fell out over the issue and the Us are still pressing for compensation from their East Anglian rivals over the matter.
However, Lambert, who was given a hot reception by the Colchester fans, guided Norwich to a stunning win at the Weston Homes Community Stadium which saw them close the gap on leaders Leeds to three points.
"We were worthy winners," said the Canaries boss. "The lads were brilliant considering all that has gone on and everything that has been said. I knew it was going to be like that.
"I've played up in Glasgow as everybody knows but it wasn't about me. I'm pretty sure that it was a sweet win for the fans. They have been exceptional and I know how quickly that can change in football. You know you're not going to last forever but we'll do our utmost to try and get this club up."