The Uzbekistan international scored with a header in the 19th minute to earn his side their second win of the group stages before Bunyodkor were forced to hold out against a second-half onslaught from the home side.
Sepahan showed their attacking intentions right from the first whistle and should have taken the lead after seven minutes when Rasoul Khatibi received a cross from the left before volleying over the crossbar.
The pressure from Sepahan continued but they were nearly punished on 12 minutes when Shavkat Salomov tried his luck with a shot from distance but the ball went wide of the left upright.
However, with 19 minutes on the clock Bunyodkor took the lead. AFC Player of the year Server Djeparov sent in his corner from the left and Kapadze had enough time and space to head beyond Sepahan goalkeeper Rahman Ahmadi.
Bunyodkor should have doubled their advantage five minutes before the break after a neat pass from Rivaldo found Salomov but, with only the goalkeeper to beat, the forward saw his effort collected by Ahmadi
The Uzbek side picked up where they left off at the start of the second half with Rivaldo forcing Ahmadi into action two minutes after the restart with a well-struck free kick while at the other end Ahmad Jamshidian forced a fine save out of Pavel Bugalo.
Sepahan continued to crank up the pressure in the remaining minutes as they sought the equaliser, laying siege on Bugalo’s goal but failing to create any notable opportunities.
They were almost made to pay for being incapable of unlocking the visitors’ defence with four minutes remaining when Rivaldo missed a golden chance ot put the result beyond doubt, only for the Brazilian’s effort to find the arms of Ahmadi.
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Sepahan coach Farhad Kazemi was furious with his charges after their 1-0 defeat at home to Uzbekistan's Bunyodkor which leaves the Iranians in real danger of not making the knock-out stages.
Timur Kapadze scored the only goal of the game in the first half, but according to Kazemi, Sepahan were fortunate to concede just the one goal.
"We made tactical errors and we were lucky not to concede four goals," he said.
"We were terrible today. We couldn't even hold on to the ball for five minutes.”
Kazemi was shocked by his team’s the performance given Sepahan were within 15 minutes of beating Bunyodkor in Tashkent two weeks ago.
"A team can't just do a 180-degree turn and play so badly after its last performance but this was us,” he said.
"We didn't even have a proper chance in the whole game…just a possible penalty shout which the referee turned down anyway.
"The players couldn't carry out our instructions, although the tactics we'd chosen didn't suit the players. I was second best tactically.”
But not all of Kazemi's wrath was directed at himself and his players, with the coach expressing his disappointment at the home fans for calling for his head during the match.
"In Uzbekistan, when they (Bunyodkor) went behind, their fans got behind them causing us to defend deeper and deeper till they scored but today, unfortunately from the 30th minute the atmosphere inside the stadium got worse and worse and the fans didn't support us," he said.
The defeat leaves Sepahan three points behind the Uzbeks in Group D and looking like suffering a second successive elimination at the group stage.
"We have to win both (remaining) matches against Ettifaq and Al Shabab to go through," said a despondent Kazemi.
His counterpart, Khikmat Irgashev, was in altogether higher spirits.
"This began as a difficult match for both teams but we changed our tactics early on and managed to score," he said.
"We made good decisions at crucial times which is what I think made the difference. After this win we're very hopeful of qualifying for the next round."