In front of a dismal crowd of little more than 1,000, Lowe struck the only goal of the game four minutes before the half-time interval.
Colin Murdock was ruled to have brought down Kevin Ellison in the Stanley area and Lowe tucked the resulting spot-kick past home keeper Kenny Arthur.
Lowe had earlier been denied by the legs of the alert Arthur, while Murdock had had his side's best chance, heading over the top of James Spencer's crossbar.
On-loan keeper Spencer tipped over a blistering drive from Robbie Williams and his efforts were made all the more important when Lowe struck.
City dominated in the second period, clearly displaying a desire to secure a victory that was lacking from the home side.
Ellison was denied by an upright and teenage substitute Ben Jones then passed up two chances to make the game safe.
However, Chester held on to register a vital victory that gives Mark Wright's side renewed hope for the closing weeks of the campaign.