Winger Sebastian Cancelliere also scored two tries -- one set up by a brilliant jinking run by Boffelli -- while Santiago Carreras crossed in the final minute for the home side, whose victory ensured that all four hosts for the quarter-finals were decided with one week left in the regular season.
The Canterbury Crusaders sealed top spot throughout the playoffs with a 66-0 demolition of the Melbourne Rebels in Christchurch, while the ACT Brumbies clinched the Australian conference with a 35-24 win over the New South Wales Waratahs.
The Wellington Hurricanes, who have the second-best points tally behind the Crusaders, sealed the fourth home quarter-final with a 37-17 win over the Lions.
The Jaguares made last year's playoffs for the first time since joining the competition in 2016 by finishing seventh but lost 40-23 to the Lions in the quarter-final in Johannesburg.
Having taken control of the South African conference on their recent tour of Australasia when they won three of their four games, they showed they had no intention of having to leave their Jose Amalfitani base again.
They were clinical against the South Africans, building phases and controlling possession, while they scrambled on defence and dominated the breakdown.
The Sharks were also heavily penalised by referee Nic Briant, allowing the South Americans to relieve pressure and control field position.
The Jaguares could have been ahead by more than 12-0 at halftime had flyhalf Diaz Bonilla landed any of the three successive penalty attempts he had late in the first half.
Boffelli produced two pieces of individual brilliance in the second half to score his second try when he outjumped Sharks defenders contesting a high kick and sprinted away.
He then exploited a group of tired Sharks forwards milling around in midfield to set up Cancelliere's second.
Centre Andre Esterhuizen scored a late consolation try for the Sharks, with Curwin Bosch's 69th-minute conversion the first shot at goal the visitors had.
(Reporting by Greg Stutchbury in Wellington; Editing by Ed Osmond)
