The Brazilian converted from the spot four minutes before half-time after being felled inside the area to send the Uzbek double winners through to the last eight.
Group B winners Piroozi struggled to find a response in the second-half as the Iranian side were frustrated by a well organised visiting defence.
The contest began at a frantic pace with Bunyodkor and Rivaldo enjoying early dominance and after eight minutes Server Djeparov crossed for Ulugbek Bakaev to head over at the far post.
The visitors continued to dominate and had another chance as Brazilian full-back Edson Ramos was denied by the legs of Piroozi goalkeeper Misagh Memarzadeh after Rivaldo’s shot from the edge of the area deflected into his path on the edge of the six yard area.
After injured Bunyodkor centre-back Gochguly Gochguliyev had to be replaced by the towering figure of Bakhtiyor Ashurmatov, Rivaldo guided a header wide midway through the first half before Timur Kapadze tried his luck from the edge of the area.
Captain Ali Karimi had the home side’s first real chance as his dipping free-kick from the edge of the area just failed to find a way under the crossbar.
But four minutes before the break Bunyodkor broke the deadlock as Rivaldo calmly converted from the spot after going to ground while under pressure from Sepehr Heydari and Nabiollah Bagheriha as he looked to turn on the edge of the area.
A minute before the break Murotjon Zukhurov preserved his side’s lead as he produced an athletic dive to turn away Bagheriha’s header which looked destined for the bottom corner from Karimi’s inviting cross before beating away the defender’s shot in first half stoppage time.
Alireza Vahedi Nikbakht headed wide for the home just after the break as Piroozi made an encouraging start to the second half with Bunyodkor happy to threaten on the counterattack to preserve their slender lead.
With 20 minutes remaining Piroozi still had failed to create a clear-cut opportunity and Rivaldo had a chance to seal the win minutes later following another Bunyodkor counterattack but was blocked out as he attempted to shoot despite Jasur Hasanov being unmarked inside the area.
Memarzadeh denied Bunyodkor’s Azizbek Haydarov with six minutes remaining, while Piroozi had only Karimi’s blocked shot in the closing stages to show for their efforts as Iran’s last surviving representatives in the AFC Champions League bowed out tamely.