It was the Seadogs' third defeat in a week and manager Jono Greening described it as one of the worst performances in his spell as boss.
Visitors Marine grabbed the lead on the hour, at the Mounting Systems Stadium, on Saturday.
The prolific Steve Walker looked to have rescued a point, when he equalised, three minutes from time.
However, the Merseyside visitors netted a 96th-minute winner.
Greening spoke to SAFC TV after the game:
"We didn't deserve a point. We didn't deserve any points. We were poor. I thought we were poor in possession, poor out of possession. We didn't do what we wanted to do. We looked a bit lethargic. We had probably six or seven players off it. Maybe it's the three games in a week. We've lost another player to there with Lewi doing his hamstring.
"We lost Wellsy last week with his ankle. We've still got Jake out, Benno out. Obviously, purpose is missing today through suspension, so we, we've got four or five lads out normally start starting again, but the performance today, listen, that was still a really good team out there. It is probably up there with one of the worst performances in the last four and a half years for me, personally."
Boro are back in action, next Saturday, at Worksop Town.
There's live commentary on This Is The Coast Extra from 3pm.
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