Gerken produced three wonder saves in the second half to earn a precious point for Geraint Williams' men although the Essex club remained stuck at the foot of the Championship table.
The Saints had begun strongly and they took the lead after 20 minutes, making the most of some good fortune when defender Danny Granville's ricochet dropped at the feet of Stern John. The experienced striker miss hit his shot, but team-mate Jhon Viafara was on hand to divert home from the edge of the six-yard box.
It was Viafara's third goal of the season, but Colchester came back strongly and almost netted an equaliser in first-half stoppage time.
Defender Adam Virgo's accurate shot was cleared off the goal line by midfielder Jason Euell.
However, the hosts were level just two minutes into the second half. It was a case of the wingers combining with Mark Yeates floating over a cross for Kevin McLeod to cushion his header down to the near post, where striker Clive Platt made no mistake.
This was Platt's seventh goal of the campaign, but Colchester could not go on to record what would have been only their fifth win of the season.
Instead it was Southampton who finished the stronger. Gerken had shot to prominence when palming away a goalbound drive from striker Bradley Wright-Phillips around the hour mark, and he then drew plaudits from both managers for his late saves.
Substitute Grzegorz Rasiak looked destined to score when rising unmarked to head across goalwards, only for Gerken to divert the ball over the bar with a reflex save.
There was even better to come in the last minute of normal time when centre-half Andrew Davies was thwarted twice by Gerken, the first with a header that nearly crossed the line before the U's keeper managed to stretch back and claw it away.
Rasiak bundled home the loose ball, but the assistant referee had already raised his flat for offside.
Colchester had a chance to steal the points themselves in the fourth and final minute of stoppage time. Johnnie Jackson headed downwards but keeper Kelvin Davis was a match for the effort, helping the ball over the bar.