Lee and Molinari were part of a four-way tie for first after the first round and both were 4-under-par in the second round. They are at 11-under-par 132 for the tournament.
Molinari had five birdies in a 4-under 68 on the East Course of the Royal Johannesburg and Kensington Golf Club while Lee had one bogey en route to a 67 on the East Course.
Each player plays the East or West Course on Thursday and Friday with the tournament playing the weekend on the East Course. The West Course is considered the easier of the two.
David Horsey, on the West Course, fired an 8-under 63 Friday and is in a tie with George Coetzee, who had a East Course score of 68, for third at 10-under.
Seven players enter the weekend at 9-under. That group includes Alastair Forsyth and Justin Walters, who were tied with Lee and Molinari for first after Thursday's play. Forsyth and Walters played the East Course Friday and shot 2-under 70s.
Lee had four birdies, including on the par 3 Nos. 5 and 8, in the first eight holes he played Friday. He had a bogey at the 12th hole but got back to 4-under on the day with a birdie at 14.
Molinari opened Friday with a birdie but gave the stroke right back at the par-3 second. He was bogey-free the rest of the he day, however.