The MLS side came off second best with a 4-3 penalty shootout defeat to Japanese side Vissel Kobe on Wednesday following a 0-0 draw - the franchise's third loss in four tour matches.
Miami were bolstered by the return of Lionel Messi who picked up a hip adductor injury during the Saudi Arabia leg of the tour.
Boss Tata Martino was able to call upon the experience of ex-Barcelona trio Luis Suarez, Sergio Busquets and Jordi Alba but were unable to help Miami finish the tour on a high.
The shootout defeat follows a 6-0 thrashing at the hands of Cristiano Ronaldo's Al-Nassr last week and a 4-3 defeat to Saudi Pro League leaders Al-Alhi.
Miami's only tour win came in a 4-1 win against a Hong Kong XI which featured none of the former Barcelona quartet from the start.
Reda more on Lionel Messi
Lionel Messi appeared with NFL royalty in Super Bowl advert and is getting paid very well
Fans pay £8k for Messi and Ronaldo's last dance, but Al Nassr man has to watch from stands
Messi missed the match in Hong Kong, leaving fans and local officials displeased. The Argentine's failure to take to the pitch sparked chants of 'Where is Messi?' and boos from the fans.
Jeers were also reserved for Inter Miami co-owner David Beckham whose attempts to thank supporters fell on deaf ears.
Messi was eager to play in Wednesday's clash following the disappointment in Hong Kong and made an appearance for the final 30 minutes.
And the 36-year-old turned on the style at the Japan National Stadium, much to the delight of the sold-out crowd in Tokyo.
Most read in Football
Thomas Frank gives honest answer on Ivan Toney's future which Arsenal fans will love
Man United legend Roy Keane names two teams who made him question if he was good enough
Ratcliffe wants to build 'Wembley of the North' but gets warning about Arsenal atmosphere
Neal Maupay is a wind-up but tactics had nothing on Nemanja Vidic and Craig Bellamy
But the seven-time Ballon d'Or winner has found going tough during the gruelling tour and admits he is ready to return home.
"I'm a little tired from this whole tour. I have a desire to finish up the last game and to return home," Messi said during a news conference.
Lionel Messi controls pass from Dan Marino as Ted Lasso watches on in Super Bowl advert
Inter Miami face one final pre-season match when Messi's boyhood club Newell's Old Boys head to Florida on February 16, before a home clash with Real Salt Lake kicks off the 2024 MLS season on February 22.