The Shakers are already relegated and could only name two substitutes against Scunthorpe due to their severe financial problems.
Goals from on-loan Peterborough duo Jonson Clarke-Harris and Nicky Ajose earned Bury a 2-1 win against the Iron, but Shirtliff said: "That's the situation we're in. We are down to the bare bones and the lads will keep going.
"You never know, we might win the last two games. I'm a big believer that the way you finish one season is how you start the next one, so hopefully we can finish on a high.
"It is a consolation but I'm pleased for the players because they've tried hard all season and haven't had the best of fortune.
"They showed a good enthusiasm in the second half to win the game.
"It speaks well of them. They're playing individually for their careers and collectively for each other, so that was pleasing.
"They've always given it a go but have just fallen short at the last hurdle.
"We gave the ball away too much in the first half so they caught us a few times on that but we did a lot better in the second half."