The Saints, who were given a stay of execution over their possible ten-point deduction earlier in the day, were heading for undeserved defeat until the on-loan centre-half stepped up with a minute of normal time remaining to smash a stunning 30-yard free-kick past keeper Scott Loach.
It was no more than the visitors deserved, but they still should have left Vicarage Road with nothing because, in stoppage time, Tommy Smith set up another loan player, Tottenham Hotspur's Danny Rose, with what looked to be the easiest of chances, but he failed to make contact when an open goal gaped before him.
The evening had started well for Roda JC's Saeijs, because he rose unmarked to meet Ryan Smith's in-swinging free-kick to head his side ahead in the 13th minute.
The visitors' advantage though was to last only nine minutes as a young Latvian left winger marked his full Watford debut in memorable fashion.
The on-loan Aleksandrs Cauna had been restricted to a single substitute appearance since arriving from Skonto Riga in January, but in the 22nd minute he surprised keeper Kelvin Davis with an angled left-footed drive after Tamas Priskin had picked him out in the penalty area following a quick Lloyd Doyley throw.
To Southampton's credit, they asked most of the attacking questions after conceding, but a period midway through the second half summed up why their plight is looking so bleak on the pitch, let alone potentially off it.
The visitors should have taken a 2-1 lead when substitute Marek Saganowski flicked the ball through to the unmarked Jason Euell, but he fired straight at Loach.
Watford's almost instant response was to go up the other end and win a corner from which Jobi McAnuff found the unmarked Mike Williamson, who headed on for the equally poorly picked up Priskin to power in his 13th of the season with his forehead.
It looked like Watford were heading for the win that would effectively guarantee their Championship status, but Saeijs was to have other ideas.