Tranmere benefited from Sheffield United’s postponed game against Brentford due to the snow by climbing above Sheffield United in the table.
Stevenage, however, have now lost 15 in 19 matches and the managerless club slip to 15th in the league.
Zoumana Bakayogo scored twice for Tranmere in the 3-1 win, their first victory in three games.
Stevenage wasted a number of golden opportunities, especially late on, and were made to pay by the clinical hosts.
Bakayogo scored the opener on 10 minutes after Stevenage goalkeeper Steve Arnold dropped an Abdulai Bell-Baggie cross into the defender’s path.
Luke Freeman equalised for the visitors with a free-kick just two minutes later after Lucas Akins had been fouled.
However, Ben Gibson put Tranmere back in front on 16 minutes after Stevenage failed to clear a set-piece.
Tranmere were 3-1 up before half-time. Bakayogo capitalised on some miscommunication in the leaky Stevenage backline and ran on the end of a long through ball to coolly slot past Arnold.
Akpa Akpro almost added a fourth goal for Tranmere in a second-half in which the hosts rarely threatened.
Instead, Robin Shroot and Sam Hoskins rued missed chances at the other end for Stevenage and they slumped to a fourth loss in five games.
While Stevenage look over their shoulders in the league, Tranmere move above Yeovil, who could only draw on Saturday, and Sheffield United in the table.