The Mexican player brought down Hulk on the edge of the Porto area in the fourth minute and two minutes later ran out of the defensive wall too early to charge down Hulk's free kick, earning a second booking.
Hulk was a constant threat at the Stadium of the Dragon, where he scored a club record 44 goals during a four-year spell before moving to Russia last year.
But Porto came closest to scoring in the first half as Lucho Gonzalez hit the Zenit woodwork with a thundering right-foot shot in the 20th.
Helton produced a spectacular save to deny Hulk in the 57th after a blunder by defender Nicolas Otamendi gifted Zenit the ball.
Porto kept up the pressure, though Hulk's blistering left-foot shots in the 65th and 70th looked set the break the deadlock before Helton once again proved equal to the tests.
Silvestre Varela's curling shot bounced on the Zenit crossbar in the 78th.