James O'Conner produced an inspired first half kicking performance for the Rebels, punishing the Highlanders high penalty count by converting four out of his first five kicks.
But the Highlanders replied with some style of their own, Thomson and Smith both finding space out wide to touch down, after sustained series of pressure on the Rebels defence.
Locked 12-12 at halftime, Jamie Joseph's halftime talk had the desired effect as the Highlanders came out flying, Thomson touching down for his second within two minutes of the restart to give the Highlanders a five point lead.
Two minutes later Poki increased the margin, getting on the end of a clever Aaron Smith box-kick to touch down in the corner, before Chris Noakes completed the difficult wide conversion.
A converted try from skipper Mackintosh was complimented by Ben Smith's second of the evening before Aaron Thomson got his hat-trick, increasing the gap to 31 points.
Highlanders 43 (Adam Thomson 3, Ben Smith, Kade Poki, Jamie Mackintosh tries, Chris Noakes 4 con) Rebels 12 (James O'Connor 4 pen)