The Gers boss praised his side for their character and level of performance but admitted some disappointment that they were unable to convert one of their late chances to take the victory.
Speaking to RangersTV at full-time, he said: “I am pleased with their performance, pleased with their attitude and I think on another day maybe one of the chances we created would've gone in.
“We are a bit disappointed at not winning the game but the level of performance and attitude was fantastic.
“I think the way we handled the ball was pleasing. We knew that City would come and press us, we knew they would go from back to front but I think some of the performances in the central area were great, we really handled the ball, managed to find that out ball, make switches of play and create chances.
“Whether we go 1-0 down or 1-0 up the same rules apply, there is an absolute belief in the squad there's a trust in each other and I think you could see it tonight on the pitch.”
Thomson believes it came down to fine margins at Petershill Park this afternoon but is happy with how his squad is progressing this campaign.
He continued: “We train at a level, and you can see that they are getting more robust, they’re stronger and I think the bit for me is we have an absolute eagerness. They were pushing themselves beyond what they have ever done, and I can't stress it enough.
“Their application was great, technically we were good on the ball and especially in the second-half we dominated the game, but it is the fine margins and we need to then put the ball in the net.”