Whelan met a Alex Greenwood corner in the 66th minute to break the deadlock, the Lady Magpies' only meaningful effort on goal during the game.
Asisat Oshoala was twice denied by Notts' Carly Telford before the break.
Nicole Rolser also went close for the Reds before Whelan's winner lifted Notts up to third in table.
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Victory extended the Lady Magpies' unbeaten run to seven matches and moved them to within one point second-placed Arsenal in the women's Super League One standings.
Liverpool are fifth with six points from five games this season, heading into the nine-week World Cup break.
Notts County Ladies manager Rick Passmoor told BBC Sport.
"Today was a win in a very different style to what we have done before. If Liverpool took their chances early doors it could have been so different.
"We found it tough at times because of how well they played in the first half. It was a real tight contest between two top teams.
"It was a hard-earned victory, but what a way to go into the break - three points, a clean sheet and top three in the table."
Liverpool Ladies manager Matt Beard told BBC Sport:
"We had enough chances to win two games today if I'm honest.
"It is something that is getting frustrating now because the same thing happened at Chelsea. They didn't really cause us any problems throughout the 90 minutes.
"Once they got in front they managed the game really well. I was disappointed with our reaction and I told the players that after the game."
Notts County Ladies: Telford, Greenwood, F Whelan, Bassett (capt), Walton, Buet, Crichton, Whelan (Susi 61), Williams, Clarke (Turner 77), White
Substitutes not used: Draycott, Plumptre, O'Neill
Liverpool Ladies: Stout, Harris, Williams, Bonner (capt), Longhurst, Dowie, Smorsgard (Rolser 45), Easton (Zelam 76), Oshoala, Schroder (Ryland 69), Murray
Substitutes not used: Danielle Gibbons
Attendance: 2,057
Referee: Thomas Brammall-Ross
Fern Whelan scored the only goal as Notts County beat defending champions Liverpool in front of a club record crowd of 2,057 at Meadow Lane.