It is possible to do it by normal bus...it will be a long day but doable as long as you are only going to visit the Sanctuary, and spend few hours on pilgrimage.
Eva Transportes have a bus departure (Mondays to Fridays) from Lagos Bus Station at 05:45 arriving Lisbon Sete Rios Bus Station at 09:30.
There is a Rede Expressos bus leaving Lisbon Sete Rios Bus Station at 10:30 arriving Fatima at 11:55h.
For the return there is a Rede Expressos Bus from Fatima at 16:30 h arriving Lisbon Sete Rios at 18:00 h.
There is an Eva Transportes bus from arriving Lisbon Sete Rios at 18:30 arriving Lagos Bus Station at 22:15. There is one bus after this at 20:30 if you miss this one.
Rede Expressos Website (Only Portuguese)- http://www.rede-expressos.pt/0010.asp
Eva Transportes -
http://www.eva-bus.com
Return Trip should cost about e 55.00 per person.