Hayes had been absent for six weeks following emergency surgery but was back on the touchline Sunday to guide the Blues to a comfortable victory that moves above Arsenal.
Chelsea are now three points clear of the Gunners, whose 100 per cent start to the season ended as they lost 3-2 to Manchester United at Emirates Stadium on Saturday.
In front of a record home crowd for Chelsea Women, they cruised past Tottenham thanks to first-half goals from Sam Kerr, Erin Cuthbert and Guro Reiten.
On the return of Hayes, Chelsea forward Lauren James said: “It was brilliant to have her back.
“It means a lot. We have a great group of staff that filled in while she was away but we are happy to have her back, and back healthy.”