During a game against Austrian club FC Red Bull Salzburg, Hapoel Tel Aviv's Itay Shechter scored after a very nice run, proceeded to pull a yarmulke out of his sock, (apparently) said a prayer—and was immediately given a yellow card.
Update: Per commenter OutKukoced:
According to this article in the Israeli newspaper Maariv (in Hebrew), people were chanting "Go to the gas chambers" in the first half (as heard by one of the team owners). [www.nrg.co.il]
According to this interview (sorry, it's in Hebrew) with Schechter [www.haaretz.co.il] the celebration was, however, not a reaction to anti-Semitic chants, as he did not hear any by that point in the game. He says, however, that afterward (unclear if he means after the game or celebration), he was made aware of the anti-Semitic insults from the stands. According to him, he was given the kipa by a fan for good luck at the airport, and decided right before the game started to keep it in his sock and take it out if he scored.
So, yes, there were anti-Semitic chants going on (par for the course at European soccer games), but no, the celebration was not a reaction to the fans.
And thus ends Kipa-gate.