Wilkinson scored in the fourth minute of injury time, after Smith connected in the 90th, to deny Mexico its first win at a World Cup. But both teams were eliminated from advancing.
Stephany Mayor gave Mexico the perfect start when she scored in the 2nd minute, and Maribel Dominguez made it 2-0 in the 29th.
Mexico needed a high-scoring win and a favor from Japan to make the quarterfinals, but England's 2-0 win in the other Group B game eliminated Mexico.
New Zealand, already out of contention, made a sloppy start at Rhein-Neckar-Arena, losing the ball in midfield. Dominguez needed no further invitation to slip a precise pass for Mayor to give Mexico the quick start.
Dominguez, the Mexico captain, ran on to a pass from Veronica Perez before curling a wonderful strike past the helpless Jenny Bindon in goal for Mexico's second.
New Zealand looked short of ideas going forward and rarely troubled the Mexican defense.
New Zealand's Ali Riley earned a corner kick with a long-range effort in the 41st, before Anna Green's 30-yard free kick was easily stopped by goalkeeper Cecilia Santiago.
The Kiwis improved in the second half and deservedly pulled one back when Smith scored off a corner. It looked like no more than a late consolation prize until Riley crossed for Wilkinson's dramatic equalizer.