Striker Jota scored their first goal in Europe for 14,176 days to put Wolves on course for victory in their Europa League second qualifying round first-leg tie at Molineux.
Vinagre's injury-time goal, after goalkeeper Sean O'Neill's mistake, then added breathing space for dominant Wolves ahead of next week's second leg in Belfast.
Crusaders will take heart from their display at Molineux, where they refused to roll over, but Vinagre's goal is likely to have put the tie out of reach.
It was Wolves' first European appearance since October 1980, when they lost 3-2 on aggregate to PSV, but there was little expectation they would be beaten by the Northern Irish outfit.
The near-miss woke Wolves up and Joao Moutinho's low effort was gathered by O'Neill before Jota dragged wide after 10 minutes.
O'Neill claimed two Gibbs-White headers as the hosts finally began to make the running with livewire Jota the chief threat.
Wolves dominated possession with Patricio a spectator but combative and compact Crusaders, who finished fourth in the Danske Bank Premiership last season, would not go quietly.
They remained a worthy opponent in a game of attack versus defence and O'Neill parried Dendoncker's long-range effort after 23 minutes.
The disciplined visitors had begun to frustrate Molineux but their resistance was finally broken after 37 minutes.
Wolves had been patient in their build-up all evening and another slow move involving Moutinho, Dendoncker and Adama Traore ended when the latter crossed for Jota to blast an unstoppable half-volley in from 12 yards.
It was deserved and the 22-year-old should have had a second two minutes later when Ruben Neves' shot deflected into his path but O'Neill blocked his low strike.
Wolves looked for a second to kill the game, and possibly the tie, and two minutes after the break Dendoncker's shot deflected wide.
It remained one-way traffic and the hosts' desire to extend their advantage was underlined when £32million record buy Raul Jimenez came off the bench with over half an hour left.
The striker only returned to training on Monday after helping Mexico win the Gold Cup earlier in July and he almost set up Gibbs-White for a second, only for the midfielder to glance his header wide after 63 minutes.
Jimenez's weak header was taken by O'Neill and he nodded wide as time ticked away.
But Vinagre, who signed a new five-year deal on Wednesday, added a second in stoppage time when he tapped in after O'Neill spilled Moutinho's cross.