Despite the scoreline it was a good workout for Gary Bowyer's young side, who did well to rebound from a two-goal deficit at half time only to let it slip at the end.
The opening goal of the game came just past the half hour. Following a Rovers attack in which Raheem Hanley saw his shot saved, the ball was quickly moved downfield by the Halifax goalkeeper Matt Glennon catching the Rovers defence out, Lee Gregory applying the finishing touch after Gareth Seddon's effort had struck the post.
Eight minutes later and the home side doubled their lead and again it was Rovers being caught out by quick thinking. A short corner wasn't dealt with and Danny Lowe converted.
To their credit Rovers improved after the break, Micah Evans saw an effort saved when through one on one, whilst Hugo Fernandez saw an effort brilliantly tipped over.
It appeared to be game on with five minutes remaining when Jordan Slew made it two goals in two games with a fine right-footed shot after cutting in from the left.
However any chance of a comeback was quickly extinguished as the Shaymen grabbed a third. Poor marking from a free-kick saw Dale Johnson head home unmarked.
"They were big and experienced and physically stronger than us," said Gary Bowyer.
"It was good experience for our boys and at times we passed it well."
Rovers Reserves are back in action this Wednesday when they take on Chorley at Victory Park.
ROVERS: Usai (sub Urwin 70 mins), Daly (sub Wylie 70 mins), O'Connor, Anderson, Beesley (sub Mason 70 mins), Fernandez, R. Hanley, Maclaren, Evans, Slew, Osawe (sub Haley 60 mins).
Sub not used: Cotton.