Elsewhere, 1992 winners Partizan Belgrade rekindled their hopes of reaching the last 16 with a dramatic 75-74 home victory over Lithuanians Lietuvos Rytas while Alba Berlin and Khimki Moscow advanced with contrasting victories.
Scariolo, who resigned as Spain coach on Wednesday having guided them to two successive European championship titles and the 2012 Olympic silver medal, saw Milan squander a 14-point half-time lead as Thomas Heurtel produced the game-winning shot for Caja.
Milan are fourth in their section with three wins and five defeats, ahead of Caja and Cedevita Zagreb who are breathing down their necks with two wins and six defeats apiece and two rounds left in the preliminary group stage of the 24-team competition.
Four teams from each of the four pools progress to the last 16 where they will be divided into two groups of eight.
Milan's last two games are against already-qualified Zalgiris Kaunas and holders Olympiakos Piraeus.
"It hurts to lose a game you dominated for almost 40 minutes and the fight for qualification is as uncertain as ever now," Scariolo said.
"We must beat Zalgiris at home and go to Athens with no other thought than winning although it's going to be tough and we have to work on the things we did badly against Caja who showed great pride tonight," added the coach who took over at Milan in 2011.
Forward Fernando San Emeterio led Caja with a game-high 17 points, Polish centre Maciej Lampe scored 14 and Heurtel added 11 to go with five rebounds.
Alba beat Poland's Asseco Prokom Gdynia 67-64 after nearly throwing away an 11-point lead in the last quarter while Khimki romped to a 77-53 home rout of Italians Mapooro Cantu thanks to 14 points from Croatian guard Zoran Planinic and American centre Paul Davis.
Budget cuts have left Partizan with a modest but hard-working roster and they produced a heart-stopping victory over Lietuvos in a game where both teams played in fits and starts before a fervent 7,500 crowd in the Serbian capital.
Partizan led by eight points at the end of the third quarter but an 11-0 run hauled the visitors back into the match and forced a thrilling climax, only for their guard Renaldas Seibutis to narrowly miss the game-winning shot on the buzzer.
An eruption of joy followed in the Pionir Arena as the home players stayed on the court for 10 minutes to salute their passionate fans.
"Every EuroLeague win is important for this young team and although we are almost resigned to defeat against the likes of Barcelona, we have shown we can still stand our ground against anyone," Partizan coach Dusko Vujosevic said.
"It is so important to advance into the top 16 because that means another 14 games against high-quality opposition."
Partizan have suffered narrow defeats against six-times winners CSKA Moscow and double champions Barcelona but Latvian forward Davis Bertans made sure they were not on the receiving end this time with an effervescent 14-point performance.
The 20-year-old, provisionally selected by the Indiana Pacers in the 2011 NBA draft, buried four three-pointers from five attempts and most of them came when his team were reeling.
"The important thing is we are still in with a chance of reaching the top 16 and we are now looking forward to the final two games against Barcelona and Bamberg," said Bertans.
"We played with a lot of energy which definitely came from the fans and they were so noisy I am surprised they didn't bring the house down."
Montepaschi Siena booked their passage with a 91-72 blowout of Unicaja Malaga, their fifth successive win after three opening defeats, while eight-times winners Real Madrid cruised to a 77-61 home victory over Fenerbahce.
Barcelona stretched their perfect record to eight wins after a 78-48 away mauling of Besiktas Istanbul and playmaker Vassilis Spanoulis scored 16 points to help Olympiakos to a 77-63 triumph at Zalgiris.
- Sports & Recreation
- Partizan Belgrade