Gills boss Peter Taylor admitted Saturday’s performance wasn’t the best.
John Egan’s late header separated the sides at Priestfield as the Gills saw off the challenge from Leyton Orient.
“I didn’t think it was a great game to be honest,” Taylor said.
“At times we were decent, at times we were poor. The effort and everything else has never been in question, we worked extremely hard as a team to defend at the right times and attack at the right times.
“But the quality wasn’t there enough, especially in the first half.”
The Gills beat Orient in a dramatic league game at Priestfield in mid-November and the Londoners have struggled this season.
But Taylor knew his team were up against it in the Johnstone’s Paint area semi-final tie.
“Leyton Orient are a good side,” he said.
“A lot of the players who played for them (on Saturday) were here last year and they finished off in the play-off final.
“They are going to have good character, they are going to fight hard and the boys are going to get tested.
“Us against Leyton Orient is a big, big game and again the boys grafted, they worked exceptionally hard and fought for everything.”
Egan scored his third goal in two games to clinch it for the Gills.
“I certainly won’t get bored of his goals, that is a cert,” said Taylor.
“It was a good delivery from Michael Doughty, John rose and scored a terrific goal.
“I thought the referee should have given a penalty just before that. I was amazed we didn’t get it. The challenge on Bradley was a penalty. Thankfully I think justice was served.”
The goal came from a corner as once again Taylor’s team, now unbeaten in five, punished their opponents with a set-piece.
“We have worked hard and we have done quite a lot on them,” he said.
“We have done more minutes on them than maybe we did at the start of the season and we have learned from that. Thankfully we have got some good deliverers and some people that want to score.”