Viliame Lolohea and Cooper Vuna also scored first half tries for the Tongans, who were beaten 16-15 by Georgia last week.
Samoa, who lost 24-22 to Fiji in the opening round of fixtures, again made numerous basic handling errors and had few opportunities to score against a strong Tongan defence.
The Samoans, however, were presented with an opportunity to claw back their 28-6 deficit when Tonga fell foul of referee Brendon Pickerill in the last 15 minutes with a succession of penalties and three yellow cards.
Tonga's replacement hooker Seta Sakalia was the first to be marched for a professional foul in the 68th minute, but the Samoans could only capitalise with a long-range Ed Fidow try.
Paula Ngauamo, who had to come back on for Sakalia, was then sinbinned in the final minute for a no-arms tackle before Sitiveni Mafi saw yellow for a professional foul long after the fulltime hooter that allowed Samoa's Melani Matavao to cross.
Samoa still have to qualify for next year's Rugby World Cup in Japan and face a two-legged cross-regional playoff starting in Apia on June 30 against either Portugal or Germany, who meet in Heidelberg later on Saturday.
Fiji and Georgia face off for the Pacific Nations Cup title at the same Suva venue later on Saturday with the hosts looking to seal a fourth straight victory in the competition.
(Reporting by Greg Stutchbury in Wellington; Editing by John O'Brien)
