Masaga, who had looked threatening all night, broke four desperate Highlanders tackles to score in the corner and give his side victory in a seesawing encounter.
The Highlanders tried bravely in the last 10 minutes but their passing was not accurate enough and the Chiefs' defence held.
The match was very much an arm-wrestle, with both sides giving plenty on defence, but failing to create, let alone convert, many chances on attack.
It was the sixth straight win by the Chiefs over the Highlanders.
The Highlanders would be kicking themselves for the loss as they had field position but failed to string together enough phases.
They had a crack at the line in the last five minutes but were penalised for failing to release the ball, after more than 10 phases, and the last chance was gone.
The Chiefs slowly gained some territory as the game went on, and dominated the ball in the second half, as the Highlanders looked hurried in much of their work.
Chiefs captain, and former Southland boy, Mils Muliaina almost scored halfway through the second half after charging down a kick but Highlanders winger Fetu'u Vainikolo just beat him to the ball.
The Highlanders got through a mountain of work on defence and the breakdown was a fierce contest.
Referee Matt Goddard tried to lay down the law in the first half by sending both Highlanders' hooker David Hall and Muliaina to the sin bin for illegalities at the breakdown.
But the breakdown was the usual messy affair and both sides successfully slowed the ball down to stifle attacking opportunities.
While the Highlanders secured a consolation bonus point, they will know they just need to hold on to the ball a bit longer and be more accurate in attack and the points will come.
The result puts the Highlanders 12th on the table, while the Chiefs are eighth.
In the first 40 minutes, the Highlanders dominated territory but could only get across the tryline once.
The try was a purler. Winger Ben Smith was put into the gap by Daniel Bowden and threw a 20m pass to Vainikolo, who ran 25m untouched to score.
The Highlanders had other chances, but a tough visiting defence and errors at exactly the wrong time cost the side.
Racking up 10 handling errors in the first half was costly for the home side.
The Chiefs finally got some hands on the ball after 15 minutes and got on the board on the 25 minute mark.
Masaga made ground and, after a series of phases, flanker Tanerau Latimer went over as the Highlanders ran out of defenders.
Smith made ground every time he had the ball in the first 40 minutes but was starved of possession in the second stanza.
Fullback Israel Dagg had an impressive match and looked secure under the high ball, while halfback Jimmy Cowan cleared well under considerable attack behind the ruck.
Masaga was the best for the Chiefs, and if he keeps up this form, international honours can not be far away.
Chiefs loose forwards Latimer and Liam Messam were hard runners, while halfback Toby Morland looked good on attack.
It was a mixed return for two former Highlanders in the Chiefs side.
Winger James Wilson left the field after 11 minutes, when he strained his hamstring in his first touch of the ball.
Morland required four stitches above his right eye, after running into the knee of Highlanders replacement hooker Jason Rutledge late in the first half.
