The Highlanders have muscled their way back to beat the Blues 26-20 in a desperate Kiwi Super Rugby derby in Dunedin.

Trailing 20-13 at halftime, the vastly-improved hosts slowly wrestled control of a clash between the two bottom-placed teams in the New Zealand Conference and retained the Gordon Hunter Memorial Trophy.

One of the few highlights of a scoreless second half for the Blues was the debut of cross code star Sonny Bill Williams, ending eight months out of rugby after rupturing his Achilles tendon at the Rio Olympics.

All Blacks midfield back Williams made one lightning break and offload but otherwise had little impact as the Highlanders dominated the closing stages.

It was the third successive win for the Highlanders, who improve their record to 4-3 while the Blues slip to 3-4.

Like their 16-12 defeat of the Blues when the teams met in Auckland in round four, the Highlanders were more physical than the northerners and treasured possession better.

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It continued a sorry record for the Blues in matches away to Kiwi teams. They have won just one of their last 23 such games.

After Banks landed an early penalty, the Blues took control of the first half, dominating possession to set up tries to prop Charlie Faumuina and lock Gerard Cowley-Tuioti.

Their first five-eighth Piers Francis landed all his four shots at goal but the Highlanders kept themselves in the contest late in the opening spell, with captain Ben Smith bagging a try, followed by Banks' conversion and penalty.

The home side emerged a more committed outfit after the break, exemplified by a powerhouse try to their All Blacks centre Malakai Fekitoa.

A contender for the best player on the park, Fekitoa's try was his fourth in five games against the Blues, the team who famously shed his services in 2014.

With the scores then level, penalties to Banks in the 55th and 73rd minutes pushed the Highlanders team clear of the flagging visitors, who made a glut of errors while attempting to play catch-up rugby.