The Greyhounds caught fire in the third quarter, rallying from a seven-point deficit with a 14-4 run, and JB never regained the lead in the fourth quarter to lose, 43-38.
The loss came four days after JB (9-4) won a 49-47 nail-biter in overtime, forcing Friday's playoff game for the league's first half title.
"With two of these (games) in the same week, our legs started to go away," Rockets coach Megan Swailes said. "It comes down to who reaches down and wants it a little more."
Despite being outsized, JB held its own with Shippensburg and 6-foot center Amanda Schroeder on the glass in the first half. Abby Stoner's 3-pointer with 3:43 left in the half gave the Rockets a 16-11 lead and a 20-15 halftime edge.
After Emily Stoner made a layup in transition for the first two points of the second half, Shippensburg found its shooting touch, making five jumpers over the next five minutes while taking its first lead, 29-26, with 2:01 remaining in the third quarter.
"I think fatigue set in," Swailes said. "Our zone worked in the first half, but our legs got tired in the third quarter."
The Greyhounds took a 39-35 lead with 4:17 left in the game on Katey Reed's jumper from the wing.
The Rockets closed to within one, 39-38, when Abby Stoner slashed into the lane for a short jumper.
Kristine Koziar, who led all scorers with 16 points, hit a jumper from the wing with 2:27 left to put the Greyhounds back up by three.
Kara Lehman missed a tough layup after driving down the lane with 20 seconds left, Mandy Myers missed the follow and Shippensburg got the rebound.
JB forced a turnover with 16.5 seconds left, but turned it right back over with 15.6 left. Amy Parson's two free throws with 11.7 left sealed the win for the Greyhounds.
"This puts pressure on us in the second half," Swailes said. "We've got to go out and do it again. Most teams don't get a second chance, but in the Mid Penn, you do."