Rovers carved out the bulk of the chances after Moore had targeted this match as one of four his side must win on the road if they are to make the end of season shoot-out.
Northampton manager Stuart Gray was less than happy with his own side's performance, but at least the point earned by the Cobblers keeps them clear of the relegation zone and stretches their unbeaten run to three matches.
Rovers took the lead in the 32nd minute through Bas Savage.
The striker returned to the starting line-up after what Moore described as a "miracle recovery" and the giant forward, with dyed blue hair to match his shirt, continued his happy knack of scoring against Town having hit the target at Prenton Park earlier in the season and also when playing for Brighton last season.
Savage's 32nd-minute header also brought prominence to 18-year old Danny Mayor who was making his League debut after signing on loan from Preston on Thursday.
It was Mayor who tricked his way past his man on the right before delivering the cross which Savage buried past Chris Dunn in the home goal.
Northampton could have gone ahead early on when Danny Jackman curled a free-kick wide, but it was the visitors who then called the shots with Ian Moore and Charlie Barnett racing clear on goal either side of half-time only to both miss the target.
Tranmere were made to pay for their shoddiness in front of goal when the Cobblers earned a point through the thoroughly committed Andy Holt.
He smashed a 52nd-minute piledriver past John Achterberg although much of the credit went to Colin Larkin whose positive run and pass found debutant Ikechi Anya who in turn fed Holt.
Tranmere could still have won the match but Dunn produced a brilliant reflex save to tip over Moore's header from Barnett's corner.