Flyhalf Lima Sopoaga slotted five penalty goals for the home side, who are likely to be without co-captain Smith for at least next week's clash with the Canterbury Crusaders in Dunedin.
Smith hit his head hard on the ground when contesting a high kick with Chiefs' fullback Damian McKenzie, who immediately signalled to referee Mike Fraser to halt the game.
Medical staff rushed to Smith's aid and while he was able to walk off Otago Regional Stadium, he failed the concussion checks and did not return.
Neither side was particularly cohesive though the Chiefs' defensive line speed kept them in the game as the Highlanders seemed intent on playing at a frenetic pace, at all costs, and their error-rate was far too high.
Their only first half reward was three Sopoaga penalties, while Lowe's two intercept tries that were converted by Aaron Cruden gave the Chiefs a 14-9 lead at the break.
Elliot then worked a clever move with scrumhalf Tawera Kerr-Barlow to catch a Highlanders defence napping inside their own 22-metre area to give the visitors a 21-9 lead.
Sopoaga reduced the deficit with two penalties before Cruden extended the lead again with his only penalty to give the Chiefs a nine-point lead with 12 minutes remaining.
The Chiefs defence then continued to hold fast in the final few minutes, which silenced the previously raucous crowd dominated by Otago University students.
(Reporting by Greg Stutchbury in Wellington; Editing by John O'Brien)
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