Hajrovic put the home side ahead with a cool finish past keeper Raul Lizoain after 10 minutes following a defence-splitting pass from Simone Verdi.
Aythami Artiles was left unmarked to head home a Juan Carlos Valeron free kick six minutes later, but Eibar quickly restored their advantage with Saul Berjon slotting in a David Junca cross having been given space in the penalty area.
Wakaso Mubarak equalised with a powerful 30-metre drive for Las Palmas and then Hajrovic and Escalante were given straight red cards for reckless challenges.
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Las Palmas pressed forward and Momo’s goal puts them in pole position ahead of the second leg.
“We started slowly but then played well as I think they (Eibar) did also,” Artiles told reporters.
“There were chances for both sides and I think the sendings off had an impact on the result.”
Celta Vigo's John Guidetti scored twice and Jonny Castro was also on target as they won 3-0 at third tier Cadiz, who reached the last 16 following Real Madrid's expulsion for fielding an ineligible player.
Barcelona beat Espanyol 4-1 in their first leg on Wednesday and La Liga leaders Atletico Madrid drew 1-1 with Rayo Vallecano.
(Reporting by Tim Hanlon in Barcelona, editing by Toby Davis)
