Preston reserves took the lead on 10 minutes with a goal from Jamie Proctor. Morecambe equalised in the second half through Phil Jeavons on 52 minutes.
The winner for Preston came on the hour mark with a goal from Neil Dougan after Proctor's run had split the Shrimps defence.
Group 1 table after 2 matches:
1. Tranmere 4 pts GD +3
2. Carlisle 4 pts GD +2
3. Preston 3 pts GD -1
4. Morecambe 0 pts GD -4
The winners of the three groups and best runners up will qualify for the semi final.
The last group matches are on 10 November with PNE v Tranmers and Morecambe v Carlisle.