Tranmere nearly opened the scoring during the early stages through Steve Jennings, but after goalkeeper Jake Cole made the save, Woking were able to build on his intervention by taking the lead when Dan Holman netted a header just before the half-hour mark.
The home team soon pushed for a second, with Bruno Andrade looking threatening in the final third, and five minutes before the break, they doubled their advantage when John Goddard fired into the bottom corner from 12 yards.
Tranmere had been hoping to build on Saturday's 2-1 win against Guiseley - just the second in the league in seven games - but a sixth defeat in eight outings was effectively confirmed when Holman scored his second of the evening just after the restart.
Holman was denied his hat-trick and Goddard a second by interventions from Scott Davies, but a fourth did arrive 17 minutes from time when Joe Quigley converted from the centre of the penalty box for his first goal for the club.
Tranmere grabbed a late consolation goal through James Norwood, but the home outfit were more than content with their night's work, which has earned them a second win in three days after previously going five matches without success.