Warburton scored a penalty in the first-half to give Halifax a 1-0 lead going into the break, and then scored again after the interval.
A Max Kretzschmar penalty then halved the deficit with 15 minutes remaining, before substitute Martin Woods was sent-off with eight minutes to go.
The Shaymen held on though for their 15th home league win of the season.
The win rounds off a positive week for Town, who drew with promotion rivals Solihull on Tuesday after beating Wealdstone last Saturday.
Halifax: Johnson, Debrah, Green (Summerfield 67), Warburton, Waters, McDonagh (Bird 87), Spence (Woods 72), Swaby-Neavin, Gilmour, Warren, Maher. Subs not used: Slew, Dearnley
Woking: Ross, Casey, Champion, McNerney, Nwabuokei, Effiong, Kretzschmar, Johnson (Loza 67), Oakley (Kabamba 58), Longe-King, Anderson (Roles 72). Subs not used: Smith, Annesley
Referee: Aaron Jackson
Goals: Warburton 10 (pen) 62, Kretzschmar 75 (pen)
Yellow Cards Warburton 16, Debrah 50, Kretzschmar 77, Roles 89
Red Cards: Woods 83
Attendance: 1763 (102 away)