It was a pulsating opening though it lacked cohesion from both sides.
Gradually Spurs began to keep more of the possession, the passing from Danny Murphy and Tom Huddlestone precise.
Southend remained defiant at the back and went for it the upset in the last ten minutes, but it was at the other end where Mido's header was denied superbly by the keeper.
Jermain Defoe also came close before extra-time, substitute Dimitar Berbatov was a threat, but still Southend refused to lie down.
Michael Dawson and Calum Davenport was regularly in Southend's penalty box looking to get on the end of something before the goal finally arrived.
Martin Jol: "We lost against Grimbsy and Leicester in the cups last season and came back in the dressing room in a state of shock. That could have happened again because I felt Southend played better than those teams last season and we went out on those occasions. Southend made it very difficult for us. They looked a good footballing side."
"I felt we lacked urgency in the first half, as if we had enough time to score the goals - but we didn't score and against a team like Southend the game wasn't going to open up."
"So we made it difficult for ourselves but we showed character. I would have preferred it if we'd made it easier for ourselves because it meant we had players out there who played 120 minutes."
Mido: "Yes I was thinking about penalties. It was a tough game and credit went to Southend because they did very well and were a good team. We didn't score an early goal so it became more and more difficult because they became more confident.
"We were a bit unlucky in the first half with my shot hitting the bar - which could have been a nice goal - then Danny went close with a good header and another header from Jermain.
"We created chances, although we didn't play to our best. In the end we changed formation, I went to the left and I think it was a good assist from me to Jermain winning the game."
Jermain Defoe: "I didn't fancy penalties! I would have definitely taken one, 100 per cent, but we just wanted to win the game. We knew it would be difficult, they played well, I couldn't believe they've been struggling in the Championship because they were a good side with good players.
"I thought we were professional, stayed patient and I knew we would win the game - I had a feeling.
"We got a break, it was a great ball by Mido and I just happened to be in the right place at the right time."
Calum Davenport: "All credit to Southend, they played well and were unfortunate not to take us to penalties. We kept going though and got our rewards for that.
"They got men behind the ball, stuck to their jobs and it nearly paid off for them. We were just delighted to be through and into a semi-final.
"I wouldn't have been scared to step up and put the ball on the spot. I was looking at the clock to see how long was left and it was in the back of my mind."
Source: TottenhamHotspur.com