The Brazilian headed in the opening goal on the half-hour and then fired home a stoppage-time penalty to send the Saudi Arabian giants four points clear at the top of Group B.
With the victory, the two-time winners of the Asian Club Championship eliminated their Uzbek opponents from quarter-final contention and left themselves needing only need a draw from their final Group B game at Al Kuwait in two weeks’ time to seal their passage to the knockout stage.
Pakhtakor’s 2-0 defeat to Al Hilal in Tashkent two weeks ago meant that the Uzbek side needed to win in Riyadh to keep alive their hopes of reaching the knockout stage.
Their intent was clear from the opening whistle as they energetically chased the ball at every opportunity in an attempt to knock the home side out of their stride and force mistakes from their players.
But for all of Pakhtakor’s hard running, there was very little end product and Al Hilal goalkeeper Mohammed Al Daeyea was rarely troubled in the opening half.
Nigerian striker Uche Iheruome was the busiest of the Pakhtakor players but his best opportunity was a 12th minute header that flew over, while the alert Khaled Al Thaker did well to get to a Server Djeperov free kick just before it could fell to a lurking Anvarjon Soliev.
On the half-hour, the home side would go in front when the Pakhtakor defence were caught ball-watching as Libyan midfielder Tareq El Taib floated in a cross from the left towards Rodrigo, who stole into space behind the last defender to head home his third goal in as many games.
The tricky running of Yasser Al Qahtani was causing problems for the visiting defence and the Saudi international striker nearly won a penalty for his side on 38 minutes when he appeared to be tripped in the box by Renat Bayramov only to see the referee wave away his appeals.
Pakhtakor had their best opening of the half just before the interval as Djeperov gathered the ball just outside the Al Hilal box and skimmed a low shot past Al Daeyea and just wide of the upright.
A minute into the second half, Al Qahtani threatened again as he burst down the right into the Pakhtakor box and fired a hard low drive that cannoned back off Nesterov.
With Pakhtakor looking jaded after their first-half endeavours, El Taib weaved his way past a static Islom Inomov before slamming a shot against the left upright.
The visitors’ best chance of an equaliser arrived in the 62nd minute as Soliev broke the Al Hilal offside trap for a clear run on goal. However, a heavy first touch allowed the ball to get away from the striker and Al Daeyea came off his line quickly to close down the danger and prevent a shot.
It would be the last effort of note for Pakhtakor and Al Hilal extended their lead in stoppage time as Rodrigo burst into the Pakhtakor box and was brought down by a lunging tackle by Nesterov.
The Brazalian took the spot kick himself, firing emphatically into the top left corner to all but secure his side’s passage into the last eight.