Around 50 Santander fans hurled objects including ash trays and lighters and spat at officials from both clubs gathered in the tribune at the Sardinero stadium and a security guard attempting to repel them required stitches to a head wound caused by a metal chair, police said in a statement.
"This morning the security guard in question filed the relevant complaint," the statement said.
"As soon as other possible complaints have been gathered ... an investigation will be launched to discover all the facts and identify those responsible."
There was no mention of the incidents on Santander's website on Thursday, while Almeria said a club director, Luis Guillen, had suffered a wound to his wrist and that security guards and police had been slow to react.
"I could never have imagined that something like that could happen," Almeria president Alfonso Garcia, who was at the game with his wife, said on the club's website.
"I have been in football for 12 years, I have been able to see more than 400 matches in the VIP tribune and the truth is that I have never experienced anything like it," he added.
"I don't understand how people can react like that. We asked them (security and police) to protect the tribune because they were not doing it."
The main object of the Santander fans' anger appeared to be club president Angel Lavin, who is partly blamed for the precarious financial situation of the north coast club.
The Santander players have not been paid for several months and when Wednesday's game, which ended 1-1, kicked off they stood still for around 10 seconds as a protest and only started playing when their opponents kicked the ball into touch.
Mired in bankruptcy proceedings and relegated twice in the past two seasons, Santander's future looked bleak after a capital increase in October designed to save them from ruin flopped and had to be abandoned.
Hopes of a bright future at the club increased when they were taken over in January 2011 by Indian businessman Ahsan Ali Syed, who had failed in an attempt to buy English club Blackburn Rovers the previous year.
Founder and chairman of investment company Western Gulf Advisory, Ali Syed said buying into the club had been "a dream come true" and Santander could become a "third force" in Spain to challenge Real Madrid and Barcelona.
That lofty goal quickly proved a pipe dream and Santander were relegated from La Liga at the end of the 2011-12 season after finishing 10 points adrift at the bottom of the table.
Ali Syed disappeared from view and the club's crisis deepened as they dropped down to the third tier at the end of last term.