The relegation-haunted U’s were on course to secure three precious points before substitute Hakeeb Adelakun netted a deflected stoppage-time goal to leave Colchester four points from safety with three games remaining.
Scunthorpe went ahead on the half-hour mark through Theo Robinson’s fine curling effort after the Colchester defence had failed to deal with Luke Daniels’ long kick.
Daniels tipped Gavin Massey’s fierce effort on to the crossbar before Tom Eastman equalised for Colchester with nine minutes remaining when he slammed home from six yards after Scunthorpe had failed to clear Massey’s corner.
Colchester then went ahead four minutes later through Chris Porter, who latched on to David Fox’s pass and wriggled past Marcus Williams before firing past Daniels.
But Adelakun’s late deflected looping effort flew in to deny the U’s a precious win.
Humes said: “It was a difficult game and conditions didn’t make it easy to play in.
“But the players were fantastic in the second half and worked their way back into the game.
“We eventually got our noses in front but it was a sucker-punch at the end of it with a deflected goal where the defender has got to get tighter to stop the ball going into the box.
“It’s hard to take but the game is not over until it’s over.
“We put ourselves into a great position and it hasn’t happened for us, but there are still three games to go and we have to see what we can get.
“It was difficult with everything that was going on and it wasn’t the easiest for the players.
“But they stuck together and they’ve shown that all season – they keep going and they were seconds away from getting a win.”
Scunthorpe boss Mark Robins was furious his side allowed Colchester back into the game, having led at half-time.
He said: “We coasted through things and I’m sick of us just doing enough.
“We switched off from a corner and they got an equaliser.
“I wouldn’t say it was a deserved equaliser because there were hardly any shots and hardly any efforts on goal.
“Then we switched off from a set-play and all of a sudden they got a free shot on goal and it put us 2-1 down.
“I’m frustrated and I’m angry because we haven’t performed.
“We got another point and we have to move on, but I just want to get to the end of the season, keep our status intact and then start getting things put right, because it isn’t right.
“I’m furious – we keep talking about players being good enough but they have to prove that week in, week out.
“And at some point, we have to take responsibility and I take the ultimate responsibility.”