Britt Assombalonga's 97th-minute backheel earned the visitors a share of the spoils at Priestfield.
In-form Assombalonga had earlier slotted home his 14th goal of the season to put the visitors in front but they were pegged back after half-time by Joe Martin's free-kick.
And when Cody McDonald put the hosts in front it looked like Posh were going home with nothing, until Assombalonga bagged his second in dramatic style.
But Ferguson insisted his striker's last-gasp efforts should not mask a performance that needed to be far more clinical.
"It's a bad result for us, no question. It's two points dropped. Performance-wise, we were very good at times and some of our football was excellent," he said.
"But I think this month is really pivotal. We can't afford to do that this month.
"We need to be ruthless, that's the word I used to the players. We need to kill teams off. We weren't ruthless enough when it was 1-0 and that's cost us.
"I knew second half we'd come under pressure, I said that at half-time to the players, and from looking really comfortable we started looked really uncomfortable.
"I think we could have done better with the (Joe Martin) free-kick, I'll have to see it again, and the second goal we could have done better with.
"We kept on pushing and pushing and we deserved that bit of luck (with the late leveller). It was a striker's goal from Britt. He's only 20, he played lots of games at the start of the season, he had a break and he's come back stronger."
For Peter Taylor and Gillingham it was a case of taking the positives from a draw that came so close to being a much-needed victory.
"Our effort was fantastic, which I'm very, very pleased with. But a win is never in the bag," he said.
"They're a very good passing team, Darren's building a good team there. We had to hang on in there and it was never comfortable.
"Joe's goal was a great goal, and that was good for us. We knew we had to fight like mad to get back in the game. To be fair I wasn't too unhappy with our first-half performance and we had our chances. I was disappointed with their first goal but we kept on going.
"The late goal hurt, but saying that I think Stuart Nelson also pulled off a couple of brilliant saves. As much as we're disappointed it was such a late equaliser, Peterborough opened us a lot of times and there was some last-ditch defending.
"We've got to get a few more of our decisions right when we're tired."
- Sports & Recreation
- Joe Martin
- Britt Assombalonga