The Argentina superstar took his tally to nine goals in six appearances for Miami in an entertaining semi-final at Philadelphia’s Subaru Park.
Venezuelan international Josef Martinez, Messi’s former Barcelona team-mate Jordi Alba, and substitute David Ruiz scored Miami’s other goals, with Alejandro Bedoya the lone scorer for outgunned Philadelphia.
The result means Messi will now lead Miami into the 42nd final of his career when the World Cup-style tournament for clubs from Mexico and Major League Soccer reaches its climax on Saturday. The win also guarantees Miami a place in next year’s CONCACAF Champions Cup, the top regional club tournament.
Tuesday’s semi-final in Philadelphia was in theory supposed to be the toughest assignment yet faced by Messi since he made his debut for Miami on July 21 after joining from Paris Saint-Germain.
Philadelphia are one of the strongest teams in MLS, and are third in the Eastern Conference standings while Miami are bottom of the table.
The Union have also been practically invincible at home, losing only once in their previous 38 games at Subaru Park.
But the home side were left in disarray just three minutes after kick-off as Miami took the lead.
A long ball forward from Ukrainian defender Sergii Kryvtsov sowed panic in the Union back line, and Martinez latched onto the pass before rifling a shot past diving Philadelphia goalkeeper Andre Blake.
Philadelphia should have equalised five minutes later when Hungary international Daniel Gazdag went through on goal only to shoot straight at Miami goalkeeper Drake Callender.
Gazdag had another good chance after 19 minutes, but saw his curling shot from the edge of the area fly just wide.
If that chance encouraged Philadelphia, the optimism was short-lived as Messi struck once again to punish slack Union defending.
Damion Lowe was caught napping and Martinez spun away from the defender to release Messi, who was given far too much time and space to direct a fierce low strike from outside the area into the bottom corner past Blake.
Philadelphia responded with sustained pressure, and Gazdag tested Callender from long range once more with a rasping shot on 29 minutes.
Although Union enjoyed plenty of territory and possession, it was Miami who struck the decisive blow on half-time.
Finland international Robert Taylor held the ball up well in midfield and took his time before picking out the overlapping Jordi Alba.
The former Barcelona star controlled and buried a clinical finish to leave Miami 3-0 up at the break.
Philadelphia coach Jim Curtin threw caution to the wind in the second half, tweaking his formation to add an extra attacker.
But Union squandered two good openings when Chris Donovan rounded Callender on 55 minutes but then shot over the bar.
Jakob Glesnes also wasted a gilt-edged opportunity from close range, hooking over the bar on 66 minutes.
Bedoya gave Philadelphia hope in the 73rd minute when he swept in from a chaotic corner, but Miami snuffed out any chance of a fightback when Ruiz restored the visitors’ three-goal advantage six minutes from time.
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