There seemed to be a lot of confusion in the comments as to whether Lugo's run would have counted had he tagged.  I've done a lot of umpiring (softball, but the relevant rules are the same) and thought I'd clarify.

First, it's true that a run can't score if the third out is made on the play and it's a force.  But a runner failing to tag up is NOT a force, even though you don't have to tag him.  A force play, by definition, is when a runner is forced to advance because the batter became a runner.  So there can never be a force on a caught fly.  (Technically, it's an appeal play.)  So if Lugo tags and scores before Pujols is out, his run counts.

In fact, even if Lugo doesn't tag up, if he touches home before Pujols is out his run counts, unless the Rockies appeal that he left early at third.  This is known as a "4th out appeal" and would nullify the run.  So having failed to tag up, his best bet was to continue home, touch it before Pujols is out, and hope the Rockies leave the field before appealing.  Once the entire defensive team leaves fair territory, they can't appeal and his run counts.