All 43,236 tickets had been snapped up for the last game of the domestic championship, which was organised after the wider Super Rugby competition was shut down in March.
"While this news is disappointing, we need to take a step back and be grateful for what we got, what it meant to our players, our sponsors and, most importantly, to our fans," Blues CEO Andrew Hore said.
The Crusaders had wrapped up the title with a game to spare on Sunday.
NZR confirmed the Highlanders' clash with the Wellington Hurricanes will take place as scheduled on Saturday without fans in attendance.
"We are naturally disappointed that none of our passionate supporters will be able to attend. We know the players will certainly miss that support in the stands when they play on Saturday afternoon," Highlanders CEO Roger Clark said.