The Poland forward netted from the penalty spot to open the scoring at the Allianz Arena after 12 minutes, before adding his second 15 minutes later as he curled past Georgi Bushchan.
Serge Gnabry fired in the host's third after the interval before Leroy Sane caught the Dynamo goalkeeper off guard at his near post to score the fourth.
Eric Maxim Choupo-Moting rounded out the scoring with Bayern's fifth to consolidate their Group E top spot as they look firm favourites to progress through to the next stage after two wins in as many games.
Viktor Tsygankov volleyed the first chance of the contest narrowly wide before Bushchan tipped over Lewandowski's header but problems followed from the resulting corner.
Serhiy Sydorchuk was adjudged to have handled inside the area, with Lewandowski coolly rolling the spot-kick home before Thomas Muller setup the second.
The German forward's throughball teed up Lewandowski, who found the bottom-right corner to score his 119th goal in his last 100 matches for Bayern.
Sane's left-footed drive struck the post eight minutes later, with Manuel Neuer forced into a rare save against Carlos de Pena on the stroke of half-time.
Lewandowski hooked wide as he looked for his hat-trick after half-time, with Gnabry then missing the target with a simple header following Alphonso Davies' delivery
However, Gnabry made amends on a rapid counter-attack as he smashed in off the underside of the crossbar following an offload from Sane, who added a fourth after 74 minutes as he whipped in from the left flank and caught Bushcan by surprise.
Choupo-Moting added a fifth as he headed in from Benjamin Pavard's cross as Bayern cruised to their ninth win in nine games in all competitions.