The Football Association reported "a number of incidents of racism" to UEFA after ugly scenes marred a 1-0 win for Stuart Pearce's team in the second leg of their European Championship play-off in Krusevac.
Liverpool midfielder Henderson said on The FA's website: "Everyone is delighted with the result and going to the Euros, but what happened tonight wasn't nice and is not called for in football. There was a lot of racist abuse out there from the stands and a lot going on after the game, which is hard to take for the players."
Defender Danny Rose was sent off after the final whistle after apparently responding angrily to monkey taunts from the crowd, while scuffles also broke out when supporters invaded the field moments after Connor Wickham's stoppage-time goal secured a 2-0 aggregate success and a place at next year's finals in Israel.
Henderson continued: "The players coped with the abuse really well. It's not nice. They kept their heads and were professional. I thought our players were brilliant and conducted themselves very well.
"The players completely condemn what happened. There were also stones, coins and seats getting thrown at us. I didn't understand why Danny Rose was sent off at the end - I didn't see he did anything wrong, other than get abused."
He added: "UEFA must deal with this in the right way."
A statement from the FA read: "The FA condemns both the scenes of racism and the confrontation at the final whistle during which time our players and staff were under extreme provocation.
"The FA has reported a number of incidents of racism to UEFA following the fixture.
"These were seemingly aimed at a number of England black players by the crowd. The matter is now with UEFA."
- The Football Association