The so-called supporter was facing a ban from watching his team following the incident at Queens Park Rangers's Loftus Road ground during Boro's 0-3 away win.
Video shared on social media showed a man throw a water bottle onto the pitch behind the QPR goal.
Fans talking about the incident on a forum indicated the bottle may have been taken earlier by a pitch invader.
Cleveland Police's dedicated football officer said on Twitter: "I've been asked by a few followers and can confirm the so called @Boro fan who urinated in the @QPRFC goalie bottle was arrested by colleagues from @MPSFootballUnit
"Disgusting act and I will do all I can to remove him from attending Boro games again."
The Metropolitan Police said a man was charged with throwing an item onto the pitch and will face court.
The force's football unit tweeted: "After an investigation @MPSFootballUnit can confirm that the male arrested at the @QPRFC v @Boro game yesterday has been charged with throwing an item on to the pitch.
"The male has been bailed and will appear at court next month."
Last month, a Sunderland fan was ejected from the Stadium of Light after he was thought to have defecated on his seat - although police later said he was merely drunk.