James McQuilkin and Daniel Udoh scored in four early second half minutes to give AFC Telford United a two goal cushion.
Conor Branson pulled one back for the hosts with 15 minutes to go, but the Bucks held on to bounce back from their FA Trophy exit on Saturday.
After the game Cowan heaped praise onto his side for showing the right character on the back of their cup exit.
He said: "I think it is our best win of the season in terms of the stage of the season.
"It is a massive result, coming off the back of two high energy games against Orient.
"Sometimes that can leave you depleted, and that is why we brought in some new bodies to freshen it up.
"It can go one of two ways and it went the right way, the lads showed character and how they have grown as a group.
"It is a fantastic win. Some could have forgiven the lads for lacking legs tonight but they were brilliant."
McQuilkin, playing in the number ten role again was a stand out performer who took his goal well.
Cowan added: "He did well amongst others. He showed high energy and enthusiasm and nothing phases him.
"If it is 3,500 people or one man and his dog, he wants to win football matches and it is a privilege to see him play like that.
"I thought Ellis Deeney and Dom Smith were superb, it was a good performance on the whole."
Despite conceding 15 minutes from time the Bucks saw the game out without too many hairy moments.
And Cowan admitted his side learned from the game management Leyton Orient showed in Saturday's FA Trophy cash.
He added: "We learned from a fantastic team in Orient, who were a bit more efficient.
"We could have been out of sight in the first half, but then we saw the game out and used football intelligence.
"The lads need to build on that and they did tonight and I am proud of them."
The Bucks chief also had some special praise for the supporters, who travelled to West Yorkshire in their numbers.
He added: "They were unbelievable on Saturday and you look at that tonight.
"They've got to get up for work tomorrow, pay to come here, and it is just phenomenal so I thank them for that."