Malaga's long-suffering fans have endured a roller-coaster ride since Sheikh Abdullah Al Thani, a member of the Qatar royal family, bought the Costa del Sol club in 2010 after they narrowly avoided relegation.
Hefty investment in players and the hiring of former Real Madrid and Villarreal coach Pellegrini yielded a top-four finish last term and a place in Europe's elite club competition.
However, things apparently began to unravel over the summer and while rumours Al Thani was looking to bail out went unanswered top players like Santi Cazorla were sold off to raise cash.
There appeared to be a power vacuum, with local officials keeping the club running as much in the dark as players, coaching staff, fans and journalists.
Al Thani's lieutenant eventually announced Malaga were undergoing an "internal restructuring" to bring them into line with UEFA's Financial Fair Play rules.
Outstanding debts to players, staff and other clubs began to be settled and a measure of calm returned.
The season began in mid-August and Pellegrini and his squad showed they were not distracted by institutional woes with a series of impressive performances that lifted them to first place in Champions League Group C ahead of AC Milan.
A 1-0 home win over the seven-times European Cup winners will live long in the memory of those who were at the Rosaleda.
Their dream run appeared to be coming to an end after 2004 winners Porto beat them 1-0 in last month's last 16 first leg in Portugal.
But inspired by highly-rated playmaker Isco and playing with a man extra after Porto midfielder Steven Defour was sent off just after halftime, Malaga stormed back on Wednesday to win 2-0 on the night and advance 2-1 on aggregate.
"The atmosphere in the stadium was incredible and the fans deserved a victory like this," Pellegrini said.
"It has been an unusual year," added the Chilean when questioned about Malaga's financial difficulties.
"The team deserves a lot of credit for what they have done both in the domestic league and the Champions League.
"They maintained their focus on the sporting side and had the capacity to get to grips with all the other problems.
"Then there was a positive atmosphere coming from a desire to help the club and the players deserve huge praise for that."
Malaga's success has been built around a squad mixing experienced campaigners like Argentine centre back Martin Demichelis, French midfielder Jeremy Toulalan and Paraguay forward Roque Santa Cruz and youngsters like Isco.
The talented 20-year-old, who is on the fringes of the Spanish national team, was voted by coaches the 'revelation player' of La Liga last season and he won the 'Golden Boy' trophy as the best Under-21 player in Europe.
But it is Malaga's old timers who have really underpinned their success and Santa Cruz came off the bench on Wednesday to seal their passage to the last eight.
"It's all about their personalities," Pellegrini said.
"They are all winners who have come from very important clubs who are used to Champions League success," he added.
"It is different at Malaga and I also experienced something similar at Villarreal.
"Every victory seems worth double when you are playing in the competition for the first time.
"Now we are among the eight best teams in Europe and we will do our best to get through to the semi-finals."