Killie were beaten 2-1 at home by Ross County in their last match of the season, with Longstaff completing the full 90 minutes. His team-mate Callum Roberts was an unused substitute.
Midfielder Longstaff, 19, ended up with three goals from 17 appearances - all starts - as Kilmarnock finished eighth in the Scottish Premiership. Winger Roberts, 20, started five times in all competitions and made a further six appearances from the bench.
Also drawing the curtain on his loan spell was Henri Saivet, who appeared as a 72nd-minute substitute for AS Saint-Etienne in a 3-1 defeat to AS Nancy.
Florian Thauvin, meanwhile, rounded off an impressive campaign with 90 minutes in Marseille's 1-0 home win against Bastia.
Tim Krul played both games as AZ Alkmaar beat Groningen 8-2 on aggregate - most recently a 4-1 home win - to take them a step closer to the Europa League. They now face Utrecht in a two-legged play-off final.
Kevin Mbabu played the full game as BSC Young Boys beat champions Basel 2-1 on Sunday, but Emmanuel Riviere played no part in Real Osasuna's 5-0 defeat to Seville.
Alex Gilliead was an unused substitute as Bradford were beaten 1-0 by Millwall in the League One play-off final at Wembley.