The men, aged 21 and 26, were arrested after warrants were executed at addresses in the city this morning.
They are being held in custody on suspicion of the attempted murder of a 23-year-old man in Burmantofts Street, Leeds, on Wednesday, May 9.
The victim was shot in the shoulder as he sat in the front seat of BMW which was waiting at traffic lights.
A silver Mazda 3 pulled up alongside the car before three masked men climbed out and began to attack the BMW.
The victim was driven to St James’s Hospital for treatment to the injury, which was classed as minor.
He was subsequently arrested but was later released without charge.
The Mazda was found burned out in Davies Avenue, Roundhay.
Detective Inspector Andy Farrell, of West Yorkshire Police Firearms Prevent Team, said: “Our investigation into this incident continues to progress and we anticipate making further arrests.
“We have now built up a clearer picture around the wider circumstances surrounding the shooting but are still keen to hear from anyone who has any information that could assist us.
“West Yorkshire Police will always treat the criminal use of firearms on our streets very seriously and will continue to focus our attention on identifying and bringing to justice those involved in such offences.”
Armed police previously arrested a 26-year-old man on suspicion of possession of a firearm with intent to endanger life.
Anyone with any information is asked to contact the Firearms Prevent Team via 101, quoting Operation Flowwick.
Information can also be shared via the Contact Us section of the force website or by calling the independent charity Crimestoppers anonymously on 0800 555 111.