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.
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)
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