With second-placed Porto having suffered a surprise 1-0 defeat at Maritimo on Sunday, Benfica knew a victory at Pacos de Ferreira would take them three full wins clear of their archrivals.
But Jorge Jesus' title-holders wasted that opportunity at the Estadio da Capital do Movel with veteran striker Lima missing a penalty in the first half, while Benfica also hit the woodwork twice, before Sergio Oliveira converted from the spot to secure victory for Pacos de Ferreira.
Benfica defender Eliseu produced a terrible tackle to bring down Paolo Hurtado for the home side's spot kick.
The loss saw Benfica remain on 46 points with Porto (40) in second, one point ahead of third-placed Sporting Lisbon.
Pacos de Ferreira (26 points) moved up to seventh courtesy of their first win in six.
Benfica, meanwhile, saw their seven-game winning streak in all competitions ended.
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