The trio of Ethan Mitchell, Sam Webster and Eddie Dawkins looked to have prevailed in the final over the hosts France, but were relegated back to the silver medal for a technical infringement in the changeover.
"It's a technical rule that did not affect the result or the time but it is a rule nonetheless and we have to wear it," said Cycling New Zealand head coach Dayle Cheatley.
Earlier the team sprint, defending the rainbow jersey they won in Cali last year, topped qualifiers in 42.892s, which was 0.2 seconds ahead of hosts France with Australia sixth and Olympic champions Great Britain a distant eighth.
They improved on that in the final to lead from go-to-whoa, backing up with a 42.808s, which was brought home by a stunning 12.999s final lap from Dawkins.
The French were 0.3s behind and well beaten, until the commissaries noted that Webster had overlapped Mitchell's rear wheel by a few centimetres in the changeover zone.
Lead-off rider Mitchell said the disappointment was tempered with the big picture.
"It was pretty grim at the time because we deserved that even more than we ever had. Our bad luck came around this time. It's a technical thing not a performance thing,"
Mitchell said. "It was about a tyre-width or so on the overlap and at 75kph that not a lot of leeway.
"But on the positive side, we had our fastest sea level time, we were the only team under 43 seconds in both rides and we have put nearly half a second into the rest of the world as we look towards Rio."
Cheatley said the team was taking the result in their stride.
"It should not dim what has been an outstanding opening day for us. The team sprint came as defending world champions and were the dominant team today," Cheatley said.
"Our new team pursuit men qualified top so that is the first time ever that New Zealand has qualified top at a world championship in our two targeted Olympic events.
"And the women recorded a big personal best to push for medals tomorrow also."
In the early session the quartet of Dylan Kennett, Pieter Bulling, Alex Frame and Marc Ryan, in their first competition together, topped all qualifiers in the men's 4000m team pursuit at Saint-Quentin-en-Yvelines.
The men's combination was one of the youngest in the competition with Kennett 20, Bulling and Frame both 21 and double Olympic medallist Ryan providing the all-important experience.
They were second fastest at the first kilometre in a superb 1m03s and then reeled off splits of 57 seconds, 57 seconds and 56 seconds for the remaining three kilometres to clock 3:56.421.
They were followed by the Olympic champions Great Britain in 3:57.716, Germany 3:58.861 and Switzerland 3:58.887 with defending world champions Australia only fifth.
"It was one of our best rides. All week we have been going well and everything has gone to plan," Bulling said. "We came into today's ride with a lot of confidence and we stuck to the plan and so far it has come off.
"We will go into tomorrow with more confidence again, lay it all down and hopefully come away with some rainbows."
It was the fastest time any New Zealand team pursuit combination has produced in qualifying at a world championship.
New Zealand take on Switzerland in the first round tomorrow, with the winner progressing to the gold medal ride later in the evening, while the fastest two teams from the losing semifinals and the fifth to eighth place ride-offs will contest for the bronze.
The proven quartet of Rushlee Buchanan, Lauren Ellis, Georgia Williams and Jaime Nielsen finished fourth highest qualifier in the women's 4000m team pursuit, to put then through to the first round tomorrow with a chance of medals.
The women started with a strong 1:10 opening kilometre and produced a consistent 1:04 for each remaining kilo to finish in 4:25.406. This was a significant personal best for the team at sea-level, four seconds below their time in the 2013 Oceania Championship.
Australia bested qualifiers in 4:18.135 from Olympic champions Great Britain in 4:18.207 and Canada 4:25.699.
New Zealand will meet Australia tomorrow which will provide a real test to push to the medal ride-off later in the evening.
The women's pairing of Katie Schofield and Stephanie McKenzie finished ninth in the women's 500m team sprint.
They clocked 33.715s which was only 0.1s outside the national record set in the helpful climes of Cali, to show their continued improvement on the world stage.
Tomorrow features the conclusion of the team pursuit, Dawkins and Webster back for the keirin, Schofield and McKenzie in the 500m time trial and Hawkes Bay teenager Regan Gough making his debut in the 15km scratch race.
Day 1 results:
Men Team Sprint qualifying: New Zealand (Ethan Mitchell, Sam Webster, Eddie Dawkins) 42.892, 1; France 43.072, 2; Germany 43.136, 3; Russia 43.371, 4; Netherlands 43.326, 5; Australia 43.379, 6.
Gold medal ride: France 43.136, 1; New Zealand 42.808 (REL), 2. Bronze medal: Germany 43.339, 3; Russia 43.468, 4.
Women Team Sprint qualifying: Russia 32.218, 1; China 32.562, 2; Germany 32.712, 3; Australia 32.878, 4. Also: New Zealand (Katie Schofield, Steph McKenzie) 33.715, 9.
Men 4000m Team Pursuit qualifying: New Zealand (Dylan Kennett, Pieter Bulling, Alex Frame, Marc Ryan) 3:56.421, 1; Great Britain 3:57.716, 2; Germany 3:58.861, 3; Switzerland 3:58.887, 4.
Women 4000m Team Pursuit qualifying: Australia 4:18.135, 1; Great Britain 4:18.207, 2; Canada 4:20.699, 3; New Zealand (Rushlee Buchanan, Lauren Ellis, Jaime Nielsen, Georgia Williams) 4:25.406, 4.
