The Blues have overcome the late withdrawal of All Blacks playmaker Beauden Barrett to beat the Highlanders 32-20 in Super Rugby Pacific.

Barrett was among several Blues forced out by COVID-19 in the Blues camp, with fullback Stephen Perofeta switching to replace him at five eighth.

Rookie backrower Taine Plumtree sparked a second-half rally after the Highlanders benefited from an error-ridden first-half performance by the Blues and from a penalty try at a collapsed maul to lead 13-3 at halftime at Eden Park on Friday night.

Plumtree, in only his second Super Rugby start, began the comeback in the second minute of the second half when he deflected a Highlanders' lineout throw and combined with his captain Dalton Papalii to score the Blues' first try.

He scored again seven minutes later when a poor kick out of defence by the Highlanders allowed the Blues to mount a swift counter-attack. Winger Mark Telea fended off two tacklers near the line and handed off to Plumtree who scored.

Telea, Bryce Heem and Rieko Ioane then combined for an Ioane try in the 65th-minute which put the Blues ahead 25-13 and gave them command of the match.

The Highlanders managed a 74th-minute try to Shannon Frizell which caused the Blues some late anxiety.

The Blues lost their opening match to the Hurricanes through a last-minute try and only just held on last weekend to beat the Chiefs, who missed a potentially match-winning penalty after the full-time siren.

But the Blues finally made the match safe with a try to Perofeta in the 78th minute.

The match continued for more than 10 minutes after the siren had sounded as each team chased late tries. The referee finally blew his whistle for full time in the 91st minute.

"In the first half, that's not how we wanted to start," Blues skipper Papalii said. "We knew coming into this that the Highlanders are one of the best teams at executing what they want."