The defender’s header completed a smash and grab 2-1 win for Spurs to end the hosts’ unbeaten run.
Eric Dier hit the post for Spurs in the first half but Mourinho’s men were forced to cling on before Vertonghen’s late goal.
They climbed to fifth in the Premier League, despite being second best for long spells, and have won five of Mourinho’s opening seven games.
Wolves drop to eighth and their unbeaten run, their longest in the top flight since 1962, ends after 11 games – although they have still lost just twice in their last 19 outings in all competitions.
The hosts made an industrious start but it was Spurs who scored after eight minutes.
The forward glided into the area before rifling in high from an angle for his third goal in seven games under Mourinho.
Wolves remained undaunted though and after Paulo Gazzaniga gathered Traore’s low effort they began to create openings.
Soon after Jota was denied by the recovering Davinson Sanchez after the defender’s initial mistake allowed the forward through.
Wolves continued to dominate but should have been 2-0 down nine minutes before the break.
Referee Stuart Attwell played a good advantage after Moura was fouled to allow Dier forward.
He played a cute one-two with Dele Alli to leave the midfielder with just Patricio to beat but his low strike hit the post.
It would have been harsh on Wolves, the better side without anything to show for it, and they continued push after the break.
Jota failed to turn in Traore’s cross and Gazzaniga pushed away Jimenez’s shot.
Spurs’ defence had lived dangerously, Vertonghen struggling against Traore and Sanchez occasionally cracking under pressure.
Mourinho’s men struggled to get going, even if Alli curled wide, and Wolves finally struck back after 67 minutes.
Traore had given the visitors problems all game and he made them pay, collecting Jimenez’s pass and unleashing a rocket which flew past Gazzaniga from 20 yards.
Tottenham then never looked like restoring their lead before the late drama. Harry Kane had barely been given a sniff and the England captain fired wildly wide with 11 minutes left.
Wolves remained the aggressors and Saiss’ glancing header four minutes later forced Gazzaniga into a fine stop.
But Spurs silenced the hosts in the first minute of injury time when Vertonghen nodded in Christian Eriksen’s corner.