Universitario did not play their league game against Total Chalaco on Saturday because of the ban.
"It is decided that the ADFP and Universitario settle the controversy before a court of arbitration," the FPF said in a statement when it ordered the lifting of the suspension on Monday.
The ADFP, a body that groups the 16 top flight clubs, imposed the suspension last Thursday because Universitario had struck a deal with a different airline, Star Peru, from that which sponsors the championship and provides teams with air travel to matches, LAN Peru, a subsidiary of Chile's LAN.
"The U," as the champions are popularly known, claim they were entitled to make a deal with Star Peru because the ADFP statutes say the body "cannot impose on any team the sponsorship of a specific enterprise as is the case with the Chilean airline."
The FPF said the ADFP must allow Universitario to reschedule their match with Total Chalaco and continue to take part in the championship normally while the issue goes before the three-man court of arbitration.
It ordered Universitario in the meantime not wear the logo of any commercial airline on their shirts. The ADFP imposed the ban when the champions wore the Star Peru logo on their shirts at a match last Tuesday.
Universitario fans, some wearing the team's cream shirts, held a protest march on Monday to ADFP headquarters in Lima and clashed with police.
Universitario, who were captained to the title last year by former Peru midfielder Nolberto Solano who has since resumed his career in England, have lost their three matches so far in the 2010 championship.
They have concentrated their efforts on the South American Libertadores Cup, taking seven points from three matches in Group Four.
