The Magpies pinched all three points late on through former Bucks winger Elliot Newby's deflected winner on an evening where neither side created much in front of goal.
For Jamie Vermiglio's Chorley it was a first league win of the season, while the hosts were unable to build on a victory at Darlington.
"It's really disappointing. I don't think we deserved to win the game but I don't think we deserved to lose it either," Cowan said. "It just shows the very fine margins with the deflected shot.
"I don't think we threatened them enough, I think they came and set up brilliantly. We knew they were a team in a false position, the players knew that.
"It's hard to criticise the attitude and application because we gave our all but didn't do enough to penetrate them and create enough chances. The game was very, very even.
"But it only takes one chance and just our luck they get a deflected shot going in the bottom corner.
"I'm not going to criticise the players' effort but we need to have more footballing nous and intelligence."
Telford, who are sixth in National North, went closest through a Jason Oswell header, Jordan Davies volley and Aaron Williams' late free-kick.