With heavy rain before kick-off 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 a vital block to prevent Holt scoring.
There was late drama, though, as Luke Shaw was ruled to have pushed over Holt just inside the penalty area, referee Mark Clattenburg pointing to the spot after consulting with his assistant.
Southampton, though, felt justice was served as Artur Boruc produced a decent stop down to his right to secure a well-deserved share of the points for the visitors.
Saints created the first decent opening when a low centre from Morgan Schneiderlin was beaten away by Norwich keeper Mark Bunn, who then tipped over Lallana's rising 20-yard drive.
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 and the ball fell to Lallana some 12 yards out but, with the goal at his mercy, he could only blaze over.
At the other end Japan defender Yoshida produced a superb block to prevent Holt getting on the end of Robert Snodgrass' cross after a great knockdown by Kei Kamara. Rodriguez's snapshot was then beaten away by Bunn and Rickie Lambert fired the rebound over.
There was late drama as Shaw's nudge on Holt saw Clattenburg give a penalty, which resulted in a mass confrontation between the players. Holt scored an injury-time winner against Everton a fortnight ago but this time Boruc guessed right.