With the Peruvian top flight not using aggregate scores or away goals to decide finals, a third leg was required to decider the winner of the overall championship following Wednesday's goalless draw that left the tie level 2-2 across two matches.
And the third leg at the Estadio Mansiche served up another thriller, as substitute Edinson Chavez's 113th-minute goal gave Clausura champions Cristal a 3-2 win on the night and 5-4 on aggregate.
Chavez, who replaced Maximiliano Nunez nine minutes earlier, came off the bench to help clinch Cristal's first overall championship since 2012.
Juan Aurich - the Apertura winners - made a dream start on home soil after Hernan Rengifo put the ball past Cristal goalkeeper Diego Penny in the 13th minute.
Cristal restored parity via Irven Avila three minutes before half-time, though Juan Aurich went into the break ahead thanks to Junior Viza's strike two minutes later.
The topsy-turvy clash continued in the second half as Argentinian midfielder Horacio Calcaterra equalised in the 68th minute, which ultimately forced extra-time with the tie all-square 4-4.
And Cristal substitute Chavez proved to be the hero in the second half of extra-time on a memorable night for the visitors.
