Sixth-placed Estoril, promoted this season, kept cool and resisted the home side's early pressure before striking from a Jefferson free kick 15 minutes into the second half.
Uruguay right back Maxi Pereira levelled through a neat volley 10 minutes later but Europa League finalists Benfica were wasteful up front.
Benfica had to play with 10 men in the last 10 minutes after midfielder Carlos Martins was dismissed for a second yellow card.
"The important thing is that we are leaders. That is what counts. We go to Porto to win the championship," coach Jorge Jesus told Portuguese television SportTV.
With two matches left, Benfica failed to take a decisive step towards their 33rd championship title and champions Porto ar just two points behind going into the "Classico" on Saturday.
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