The Saddlers fell behind to two first-half goals as League One Rovers started the game strong.
But Clarke’s men battled back in the second half and almost forced extra-time following Caolan Lavery’s goal and the manager was pleased with their response.
“I’m going to take confidence from the performance,” Clarke said.
“We’ve run a mid-table League One team and probably had more territory, advantage, possession and shots on target.
“I take the positives from that with a lot of key players missing.
“Eli (Elijah Adebayo) has come off his sick bed, he’s only been able to do a light session as he’s been ill Wednesday, Thursday and Friday.
“The lads are giving me everything and I’m just frustrated we didn’t perform as well as we could in the first 30 minutes than what we did in the rest of the game.
“They started bright and we probably paid them too much respect.
“We then had a lot more of the ball and if anything we probably deserved extra-time.
“But it wasn’t to be. Credit to my lads, we have a lot of injuries and illness in the camp and if you were at the game I don’t think you’d know there was a division between us.”
Striker Adebayo had a one-on-one chance on the stroke of half-time that was saved well by goalkeeper Anssi Jaakola and Clarke felt his side deserved more at half-time.
"The first 30 minutes Rovers were on top but for the next 60 (we were)," Clarke added.
"We had a great chance before half-time and plenty of chances in the second half, so we're disappointed.
"I always thought if we could get in at half-time with nothing silly given away, we could go on to win the game, but it wasn't to be."