With heavy rain before kick-off being followed by sleet, neither side was able to get any real spell of possession, with clear-cut chances few and far between.
Saints skipper Adam Lallana blasted over when in front of an open goal, while Japan defender Maya Yoshida made vital blocks to prevent Holt and Robert Snodgrass scoring.
There was late drama, though, as Luke Shaw was ruled to have pushed over Holt just inside the penalty area, as referee Mark Clattenburg pointed to the spot after consulting with his assistant.
Southampton, though, felt justice was served as Artur Boruc produced a decent stop down to his left to secure a well-deserved share of the points for the visitors.
The terrible conditions made for testing control from both teams during the opening exchanges as the ball whizzed across the saturated surface.
It was difficult for players to keep their footing, with Holt shown a yellow card on 16 minutes after sliding through on Morgan Schneiderlin.
Southampton created the first decent opening when a low centre from Schneiderlin was beaten away by Norwich keeper Mark Bunn, who then tipped over Adam Lallana's rising 20-yard drive.
Norwich - who beat Everton here with two late goals a fortnight ago - were struggling to get hold of the ball in midfield as the visitors continued to press.
When right-back Russell Martin did get forward and float in a teasing ball through the penalty area, goalkeeper Boruc got there ahead of Kei Kamara, making his first start since a loan move from Kansas City.
Southampton broke quickly on 28 minutes through Rickie Lambert and his onward pass found Gaston Ramirez in space at the edge of the Norwich penalty area, but his attempted chip was palmed out by Bunn as Javier Garrido mopped up the loose ball.
At the other end, Snodgrass whipped in a 25-yard free-kick, which Boruc fisted away.
Norwich were forced into a change nine minutes before the break when Anthony Pilkington hobbled off with a hamstring injury, replaced by Wes Hoolahan.
Holt was just unable to get on the end of a low cross from Snodgrass which flew through the Southampton six-yard box.
The visitors had a golden chance to take the lead at the start of the second half.
Jay Rodriguez burst down the left and cut into the penalty area. His cross was cleared by Sebastien Bassong, but the ball fell to Lallana some 12 yards out.
However, with the goal at his mercy, the Southampton skipper could only blaze the ball high into the Barclay End.
The pace of the match intensified as Japan defender Yoshida produced a superb block to prevent Holt getting on the end of Snodgrass' cross after a great knockdown by Kamara.
Rodriguez' snapshot was then beaten away by Bunn and Lambert fired the rebound over.
At the other end, Snodgrass was played in by Hoolahan, but the ball ran away from the Scotland international as he went around the goalkeeper, which allowed Yoshida to hack clear.
Midfielder James Ward-Prowse came on for Lallana as Southampton looked to freshen things up for the closing stages, before Norwich sent on January signing Luciano Becchio for Kamara.
There was late drama as Shaw's nudge on Holt saw Clattenburg give a penalty - which resulted in a mass confrontation between the players with substitute Jason Puncheon booked.
Holt scored an injury-time winner against Everton a fortnight ago, but there was to be no repeat as Boruc guessed right and earned Southampton a draw.