Both suspects were undergoing questioning by the police, however no details on their identities were revealed or their intentions.
“Israel Police will take determined action against any party that intends to disrupt or does disrupts the orderly course of the Pride Parade held today in Jerusalem,” they said in a statement.
Security measures were in preparation for the parade which is expected to attract a crowed of over 30,000 participants double the number from last year. Police have deployed more than 2,500 officers including Border Police, special patrol units and undercover officers.
During the 2015 Pride Parade in Jerusalem, 16-year-old attendee Shira Banki was stabbed and killed by a religious Jewish extremist.
Meanwhile, it what can be seen as a clear support for the LGBTQ community at the start of Pride Month, the Israel Police has recently hired transgender recruits who completed their training.
The police force is following in the footsteps of the Israeli military, which is considered forward thinking and was among the first to include openly transgender people among its ranks.
Police spokesman says the recruits were hired individually and serve like anyone else on the force
Israel has the most open attitude in the Middle East towards homosexuality, with a large and influential gay community. However, the conservative Jerusalem, a heavily religious city sacred to Jews, Muslims and Christians, is far less gay-friendly than liberal Tel Aviv.
Last week, the Jerusalem Municipality rebuffed a request by the city's top Ashkenazi religious figure to ban gay flags, asking the mayor in a letter to "spare us the embarrassment."
The parade also comes a day after Israel appointed its first openly gay cabinet member, with Prime Minister Benjamin Netanyahu naming Amir Ohana to the position of justice minister.