The Tykes secured their first away point of the season when Jim O'Brien capped an impressive cameo performance with an equaliser after Daryl Murphy had given Ipswich a first-half lead.
The home fans were then left baying for an injury-time penalty after Frank Nouble went over Jean Yves M'Voto's challenge - in an incident which saw Town left-back Aaron Cresswell shown a straight red card on the final whistle for continuing the protests at referee Andy D'Urso.
Flitcroft was left delighted with his side's second-half performance after a lacklustre opening 45 minutes.
The Tykes boss said: "I felt for a few weeks that we were on the verge of a good run. Our defending is improving and we have had a settled team which has certainly helped.
"We went toe-to-toe with a quality team in Ipswich and deserved a point, if not more."
Flitcroft was particularly delighted with the impact of his substitute after O'Brien's introduction proved the difference.
Barnsley were below-par in the first half as Ipswich slowly turned the screw and finally got the goal they deserved when the unmarked Murphy took advantage of sluggish defending to head home.
But Town were unable to capitalise on their lead as Barnsley improved greatly after the restart.
O'Brien's neat side-foot restored parity in the 70th minute before former Ipswich striker Scotland shot wide from a good position.
Of O'Brien's performance, Flitcroft said: "Jim was the catalyst for us to get on the front foot.
"He has trained excellently and he has supported the side while being out of the team. I was delighted with his performance."