Earlier Paddy Fleming had given the home side the lead when he fired the ball from a freekick around the defensive wall and out of goalkeeper Danny Robinson's reach for the 34th minute opener.
On the hour Waitakere captain Jake Butler levelled the scores with a shot which took a deflection before nestling in the Team Wellington goal.
With their fourth win in five outings, Waitakere now trail Auckland City only on goal difference.
City, just back from their brave effort at the Club World Cup, had the weekend off with their game against Hawkes Bay United rescheduled to February 6.
Mike Cunningham gave Otago the dream start in the deep south.
He gathered a ball from a long range freekick and blasted home from 15 metres over Canterbury goalkeeper Adam Highfield.
Determined to get back in the game, the visitors pressed but without scoring and had their hopes further dashed when golden boot front-runner George Slefendorfas was sent off with 20 minutes to play.
Waikato finished their game against YoungHeart with a full complement and with plenty to cheer about.
Turning defence into attack, they went ahead in the 27th minute when Jason Hicks scored. From another trademark breakaway, they doubled their lead on the half hour with Adam Thomas scoring an inevitable second goal.
Three minutes into the second spell and with the home team a player down following the red card for Barry Lewis for an ugly tackle, Waikato made it safe when Josh Green netted.
Late in the game Tomas Mosquera got one back for the home side when Waikato failed to clear a corner.
In the ASB Youth League semifinals, Auckland City were held 3-3 at home in normal time by Canterbury United. Canterbury won the penalty shootout 9-8 to win through to the final.
It was just as close in yesterday's second semifinal as Waitakere United came back from 2-0 down at halftime to level at 2-2 at fulltime before winning in extra time.