The Borussia Dortmund striker netted twice from the spot either side of Lukasz Piszczek's close-range strike while Lukasz Teodorczyk and Jakub Kosecki were also on the scoresheet to complete an easy night's work for the hosts, who suffered their first defeat of the campaign against Ukraine on Friday.
San Marino, meanwhile, have lost all six matches and have now shipped 29 goals in that time.
Bartosz Salamon volleyed wide from a decent position as Poland attacked from the off but it was not until the 21st minute that they went ahead, Lewandowski slotting past San Marino goalkeeper Aldo Simoncini from the spot after Alessandro Della Valle had handled in the area.
Adrian Mierzejewski fired over from the edge of the area before turning provider in the 28th minute as his cross was converted by Piszczek to give Waldemar Fornalik's men a cushion. Andy Selva wasted a gilt-edged opportunity to halve the deficit in a rare San Marino attack when he missed the target from close range.
And he was made to rue his miss when Lewandowski netted his second penalty five minutes after half-time after Della Valle was again adjudged to have handled in the box.
It was 4-0 just after the hour mark when Teodorczyk netted from Kamil Grosicki's cross, and San Marino's misery was compounded in the second minute of injury time when Kosecki latched on to Lewandowski's through ball and slotted low past Simoncini.