The Ligue 1 outfit saw their hopes of qualifying for the UEFA Champions League knockout stages ended, despite a spirited performance at the Stadio San Paolo.
Marseille broke the deadlock through Andre Ayew's 10th-minute opener, but a quickfire double from Gokhan Inler and Gonzalo Higuain saw Napoli lead at the break.
Florian Thauvin levelled proceedings in the 64th minute, but Higuain notched his second and the winner with 15 minutes remaining, meaning Marseille cannot achieve second place in Group F as they trail Arsenal and Napoli by nine points with two matches remaining.
That result saw Marseille's winless streak in all competitions extend to seven matches, but Baup believes his players are showing signs of improvement.
"We made some improvements but we still made mistakes," he said. "We have a good team who were able to score two goals in Naples but things keep going against us.
"We knew it would be hard and we gave our best. Now I must concentrate on working to continue to improve the situation. This squad does not give up.
"In this game, we can say we were not very far from getting a result, but again they scored the extra goal. However, we showed that we wanted to go for it and we had opportunities.
"We're not far away, but the outcome is not a positive one.
"It's clear that our group with Arsenal, the Premier League leaders, Napoli, who are targeting the Scudetto, and Dortmund, chasing Bayern in the Bundesliga, is a difficult section.
"We have done our best to rival them all."
Marseille will look to get back to winning ways against Sochaux in Ligue 1 on Sunday.
‘The pure simplicity of the way Slot has managed the squad is probably the biggest thing I could say about him. It’s not broken, so let’s get on with it’: Liverpool legend full of admiration for Jurgen Klopp's successor at Anfield
‘I trained at Spurs and thought they’d give me a chance. But I received a letter thanking me but saying they didn’t think I was good enough – I was gutted’: How Tottenham missed out on signing Wales legend John Toshack
