Tom Johnstone scored twice in the second period following first-half scores from Toby King and debutant Mikey Lewis.
Tonga showed they will be no pushovers as the first Pacific island nation to tour England, leading early on through Starford Toa and Tyson Frizell.
Tolutau Koula added a late score for a grandstand finish, but England held on.
The series continues in Huddersfield on 28 October, before concluding in Leeds the following weekend.
England led through their first meaningful attack when Lewis made a brilliant driving run through midfield, beating three men, before switching to the left wing where King - a Grand Final winner last weekend with Wigan - was able to power over in the corner.
But Tonga responded brilliantly, and expertly worked tries arrived through Toa, after a slick passing move, and Frizell following a clever grubber kick.
Those scores put the tourists in front, yet England reacted when Lewis scored his first international try, shaking off tacklers with a bulldozing run to score - only for Tonga to pull level at the interval through an Isaiya Katoa penalty.
Shaun Wane's side struggled to shake off the dogged Tongans, but the hosts regained the lead when Johnstone touched down in the corner following a brilliant looped pass by Jack Welsby.
At 22, Welsby became the England's youngest men's captain after being given the role because of George Williams' suspension.
Catalans winger Johnstone secured the win via an interception and breakaway try.