Messi scores off the bench as Miami progress in Jamaica
Messi, who had been rested for Miami's last three games including the first leg against Cavalier, started on the bench but came on in the 53rd minute to the delight of the crowd at the National Stadium.
The Argentine scored Miami's second with the final kick of the game, running on to a fine through ball from teenager Santiago Morales and clipping it first-time past the advancing Vinco Barclett.
With the home side's hopes of an upset win already dashed there were cheers for the goal from the Jamaican fans who were delighted to see the eight-time Ballon d'Or winner play in their country for the first time.
Miami knew an away goal would kill the tie and they began in positive mode with a long-range drive from Telasco Segovia flashing wide.
A bumpy surface made it tricky for either side to play much in the way of attractive passing football but Miami showed urgency and Luis Suarez flashed a well-struck volley just wide from a tight angle.
Miami lost midfielder David Ruiz to injury with Benjamin Cremaschi replacing him in the centre of the park but the visitors continued to press forward.
The goal came in the 37th minute when Inter's Argentine forward Tadeo Allende went down under challenge from Christopher Ainsworth and referee Keylor Villalobos pointed the spot.
Suarez confidently rattled home the penalty to give the visitor's a 3-0 lead on aggregate and a cushion of comfort that allowed them to play out the rest of the game with little stress.
The young Cavalier team, featuring several of the more promising talents from the island nation, never lost heart though, clearly determined to leave their mark on the tournament.
They almost got some reward for their efforts when substitute Kaile Auvray burst in from the left and his low shot was only kept out by a fine save at the near post from Oscar Ustari.
Then came Messi's moment, a classy finish from the 37-year-old, to cap a win that ensures Miami progress into the last eight where they will face Los Angeles FC in an all-MLS tie.