Academy pair Leigh Mills and Troy Archibald-Henville formed a new central defensive partnership to allow Charlie Lee to move forward into midfield, in place of Jamie O'Hara.
The captain was the team's inspiration in the opening 45 minutes, scoring one and having a part in the second goal, both inside the first 20 minutes.
Spurs made it 2-0 thanks to a goal from Jake Livermore who continued in central midfield, alongside Lee.
After the home side had narrowed the deficit, the closing stages were only noted for a bad tackle on Adel Taarabt which was the spark for some pushing and shoving between the two sets of players.
After last week's 4-0 reverse at home to a strong Reading line-up, Allen said: "We gave a good account of ourselves but we didn't take our chances and were punished for it."
After Allen watched his side win for the sixth time in 12 fixtures this season, he said: "We talked about it, watched a lot of footage and I thought the reaction was excellent, the boys went about it in the right way.
"The first half performance was very good, the way we moved the ball, created chances and took a two-goal lead."
Source: TottenhamHotspur.com