The midfielder wore the armband as the Young Lions capped an near-perfect qualifying campaign in the group phase of the European U21 Championship with a 3-0 victory in Tiraspol.
Tom dictated play from central midfield and the provided the icing on the cake for Spurs fans as he set-up Harry Kane for the third goal.
Gareth Southgate's team therefore completed qualifying with nine wins and a draw in 10 matches, 12 points clear of second-placed Finland.
England now go into the play-offs and the seven winners will join hosts Czech Republic in next summer's finals.
Academy graduate Tom, on loan for the season in the Premier League at Swansea, earned his ninth cap and has yet to lose in Under-21 colours, winning eight and drawing one.
"I was absolutely buzzing when the manager told me, I couldn't take the smile off my face!" he said after returning back to Swansea on Wednesday.
"We went over a few things before the game and he asked me if I'd be captain. I was delighted. Every player would want the chance to captain their country and to do it was amazing.
"I let my parents know straight away. It was a proud moment."
West Brom's Saido Berahino struck twice with Harry's second goal in as many Under-21 matches securing victory. Alex Pritchard came off the bench for his second cap as the match ended with three Spurs players on the pitch.
"It was the perfect way to finish qualifying," added Tom. "We played well, controlled the game and it was great to set-up Harry for his goal. I knew he was going to stick that chance away."
The draw for the play-offs is on Friday.