Samoa was awarded a penalty try after eight minutes for a deliberate knock-on in defense by Tonga winger 'Otulea Katoa. He also received a yellow card " one of three handed out in the match.
Samoa's lead increased to 14-0 after only 11 minutes when lock Jeff Lepa barged through the Tonga defense from an attacking lineout. After a penalty to Tonga scrumhalf Tane Takulua, Patrick Faapale kicked his third goal of the match for a 17-3 lead.
Faapale took over the No. 10 jersey from influential flyhalf Tusi Pisi who missed the match with a broken hand. He kicked two more penalties before halftime, lifting his tally for the match to 13 points.
Tonga's first half had been undermined by handling errors and disciplinary lapses but overcame those faults in the second spell, taking charge at scrums. Its lineout also became a more effective attacking platform than in the first spell.
But it still struggled to breach the Samoa defense, often finding itself thwarted on the line. It wasn't until the 61st minute that replacement Opeti Fonua crashed over after strong leadup work by Takulua and Sione Kalamafoni.
Tonga was also unable to take advantage when Samoa was reduced to 14 men. It was attacking again when Tusitala pounced on a handling error near his own 22 and dashed 80 meters to score.
"The first half was crucial for us," Samoa captain David Lemi said. "Like we did against Fiji last week, we started well but we didn't finish at the end."
Tonga captain Nili Latu was forced to leave the field injured in his 50th test.
"We got taught in the first half we can't play rugby with so many mistakes and a lack of discipline," he said.
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Samoa 30 (Jeff Lepa, Danny Tusitala tries; penalty try; Patrick Faapale 2 conversions, 3 penalties; Viliami Hakalo conversion), Tonga 10 (Opeti Fonua try; Tane Takulua conversion, penalty). HT: 23-3.