The Pacific nation had already seen three players sent to the bin when Solomon Haumono and Joe Foliaki were both given the red card for their part in a violent clash with just minutes left in the game.
However, this should not detract from what was an excellent encounter between two highly competetive teams.
Rob Purdham had opened the scoring for England after twelve minutes of pressure on the Tonga line, followed up by a try for Brett Ferres, both of which were converted by Jamie Rooney to open up a 12-0 lead.
The Tongans came back into the game with a touch down from Taniela Tuiaki followed by a well-worked try for Ali Felitei Mateo cut the deficit.
However, Mark Calderwood had the final say of the half ensuring that England were well in control at the break; but Tonga scored the first try of the second period through Tyrone Smith to keep themselves in contention.
Coach Paul Cullen was delighted with the win, saying: "I can't remember the last time I won any silverware. It's been a tough month's work but these young English players have got an awful lot out of it.”
Tonga lost their discipline towards the end of the game, responding to the deficit on the scoreboard in bad-tempered fashion on the pitch, and referee Richard Silverwood acted accordingly.
Cullen continued: "And, if the Tongans hadn't kicked up in the last five minutes, they would have got something out of this competition as well.
"I have been impressed by the way they have gone about their business apart from that nonsense at the end."
Tonga coach Jim Dymock put his players’ excitement down to pride, pointing out that it was nothing that hasn’t been seen in the Gillette Tri-Nations.
Dymock said: "The boys are very proud people. They love their country and just wanted to win. A couple of things didn't go our way and they got frustrated.
"I think they were just standing up for themselves. That's test match football, isn't it? That's what it's about, putting your heart and soul into your jumper.
"They might have gone a little overboard but nothing that you haven't seen in the Tri-Nations. I think a lot of it was push and shove and hopefully it will be swept under the carpet."