Starvation, Thirst and Suffocation

When deprived of food, water, or air, the rule of three applies. An adventurer can handle three weeks without food, three days without water, and three minutes without air outside of strenuous situations.

After that, such deprivation is a significant test of a PCs’ stamina. At the end of the time period (three weeks, three days, or three minutes), the character must succeed on a DC 20 Endurance check.

Success buys the character another day (if hungry or thirsty), or round (if unable to breathe). Then the check is repeated at DC 25, then at DC 30, and so on. When a character fails the check, he loses one healing surge and must continue to make checks. A character without healing surges who fails a check takes damage equal to his level.

In strenuous situations, such as combat, going without air is much harder. A character holding his breath during underwater combat, for example, must make a DC 20 Endurance check at the end of his turn in a round where he takes damage.

As with environmental dangers, a character cannot regain healing surges lost to starvation, thirst, or suffocation until he eats a meal, drinks, or gains access to air again, respectively.

A character with 0 or fewer hit points who continues to suffer from one of these effects keeps taking damage as described above until he dies or is rescued.

Published in Dungeon Master's Guide, page(s) 159.

I've bolded the relevant paragraph for the situation.  This is for creatures voluntarily holding their breath.  Here's what I would rule:  forcing a creature to suffocate would bring in the coup de gras rules and the damage done would be the same as an unarmed attack with no strength bonus (i.e 4 hit points of damage).  At that point the Endurance checks would start.  I would also rule that the creature would get a saving throw vs the sleep condition immediately.

If the creature is high enough level that their Endurance skill is +19 or better, it is really difficult suffocate because they cannot fail the check (at least in the first round), but they still would take damage (from the coup de gras attack).  The following rounds the DC goes up by 5, etc.  Until the creature fails the Endurance check, the creature won't take suffocation damage.  So the creature is taking maximum damage from an unarmed attack (4 hp) every round and when the creature fails the Endurance check, it takes damage equal to its level.

There are better ways to kill a helpless creature than by suffocation.