The hosts took an early lead with Mojtaba Zarei scoring just 12 minutes into the game. 30,000 spectators were present for the match at Tehran's Azadi Stadium on Thursday.
The Reds' Brazilian striker, Wesley Brasilia, doubled the lead upon a smoothly executed pass from Iraqi midfielder, Hawar Mulla Mohammed, in the thirtieth minute.
"We will go atop the IPL table if we continue to play like this," Zlatko Kranjcar, Croatian manager of Persepolis declared.
"Our team has been motivated since Habib Kashani came to Persepolis as the club's new caretaker three weeks ago," he added.
Saipa boss, Mohammad Mayelikohan, however, said Persepolis put up their best performance to date in the present league.
"We were out of luck in this match. Persepolis was a different team today and showed their best performance by taking better advantage of their opportunities," Mayelikohan said.
The victory sent Kranjcar's side to fifth place with 20 points after 13 matches while Saipa sits at 11th place on 17 points. Esteqlal, which will play Saba on Friday, currently tops the standing with 23 points.
Thursday's match results
Steel Azin 1-0 Sepahan
Teraktorsazi 1-0 Abumoslem
Shahin 2-1 Rah Ahan
Malavan 2-1 Mes