The Fifa World Cup-winning captain, who has a hamstring strain, stayed rooted to the bench throughout the 4-1 friendly win against a Hong Kong select XI.
It brought a show of anger from the near-capacity crowd of 38,323 who had paid upwards of 1,000 Hong Kong dollars ($125) to see their hero, and in many cases five times that amount.
Halfway through the second-half, chants of "We want Messi" rose around the Hong Kong Stadium from fans desperate to see the greatest footballer of his generation in the much-hyped exhibition game.
Jeers ring out
The booing became louder during the last 10 minutes when it became clear that the eight-time Ballon d'Or winner would not make even the briefest of cameos.
The jeers rose to a crescendo at the final whistle and Miami co-owner Beckham was drowned out by booing as he tried to thank the crowd for "their incredible support" while fans signalled their anger with thumbs-down gestures.
"I'm just really disappointed," fan Jonathan Wong told AFP. "Everyone is here to see Messi, so I feel a bit cheated.
"Without him it's just like another regular Hong Kong Premier League match, where a ticket only costs HK$80 ($11). This time we paid HK$5,000 ($625).”
Miami coach Gerardo Martino said the club's medical team had taken the decision after an assessment on Sunday morning.
"We understand the disappointment of the fans for the absence of Leo (Messi)," Martino told reporters.
"We understand a lot of fans are very disappointed and we ask for their forgiveness.
"We wish we could have sent Leo on for at least a while but the risk was too big.”
The 36-year-old Messi played just six minutes in Miami's last match, in Saudi Arabia on Thursday, and now faces a race against time to be fit for the new MLS season that starts on February 21.
Bitter end to 'Messi mania’
It was a bitter end to days of Hong Kong "Messi mania”.
Tens of thousands turned up just to watch him train on Saturday, when he did little more than jog and stretch.
The team hotel was besieged by hundreds of fans trying to glimpse their hero, and a traditional junk boat was cruising around Victoria harbour with Messi's face plastered across its sails.
Messi shirts had been flying off the shelves after tickets for the match sold out in an hour when they went on sale in December.
Echoing the fans' anger, the Hong Kong government said they could withdraw their HK$16 million ($2 million) funding to the organisers that helped bring Inter Miami to the city.
"The Government, as well as all football fans, are extremely disappointed," it said in a statement.
"The organiser owes all football fans an explanation.”
Taylor opens the scoring
Robert Taylor opened the scoring for the MLS side in the 40th minute with a delightful right-foot curling shot from the left-hand edge of the box.
Two minutes later Hong Kong's Henri Anier laced a left-foot finish home to make it 1-1.
Miami regained the lead after half-time when Lawson Sunderland found the target from close range and Leonardo Campana increased the lead in the 56th minute.
Busquets and Alba finally made an appearance from the bench after 62 minutes to a smattering of cheers but Suarez was another no-show.
Ryan Sailor rounded off the scoring for Miami in the 85th minute with a glancing header.
It was Miami's first win in five matches on their globe-trotting pre-season tour, which heads to Japan for a friendly against Vissel Kobe on Wednesday.