Gavin Massey headed Colchester in front in the 20th minute after substitute Bradley Garmston had brilliantly picked him out in the area.
The U's doubled their lead four minutes later when Drey Wright finished another good attacking move, after Clinton Morrison had helped Brian Wilson's low cross into his path.
Kevin Lisbie broke the offside trap to pull a goal back for the O's eight minutes before the break, but then saw his 77th-minute penalty saved by U's goalkeeper Sam Walker after Garmston's foul on Shaun Batt.
Slade said: "The first 30 minutes of the game proved critical for us. If we'd stayed in the match and then performed as we did in the second half, then I think we would have won the game.
"I don't think we had enough tempo in the opening half hour and we were short.
"That needed to change and to be fair it did and we showed the kind of intensity after that that I was looking for.
"We got a lifeline just before half-time with Lis (Lisbie) getting us back into the game.
"We were 2-1 down going into the second half and I thought we were very good after half-time and should have got something out of the game.
"We dominated in the second period and we had chances to equalise.
"But when you've conceded two goals in the first period, you're always chasing the game and it's not easy."