Giménez parting was somewhat peculiar, he forced his immediate departure to the French team Olympique de Marseille by refusing to play against Werder Bremen.
The defenders Daniel Majstorović and Kōji Nakata were brought in to replace Lyon-bound Patrick Müller and Murat Yakın who was to retire at the end of the season.
Despite the 3-0 defeat by FC Thun in the second round, Basel started the season well and led the championship right until the last day of the league campaign.
[9] Goals in either half from David Degen and substitute Julio Hernán Rossi ensured Christian Gross's side the advantage before the return leg at the Weserstadion on 24 August.
The wayward defending continued into the second half, allowing Argentinian striker Rossi to double the home team's advantage on 52 minutes by drilling through Reinke's legs to the obvious delight of a sell-out 29,000 crowd at St. Jakob Park.
Rossi ran on to a pin-point pass from Matías Delgado with just two minutes remaining as Basel vanquished memories of their 0-2 defeat by RC Strasbourg on Matchday 1.
However, Tromsø regained their lead three minutes later when Ole Martin Årst collected Joachim Walltin's pass before hitting an angled shot into the net from 12 metres.
Having dropped to ninth spot in the domestic league, Monaco were eager to impress on the continental stage, but always appeared vulnerable against a solid Basel outfit.
The Swiss side took control of the match from the off, and went close to breaking the deadlock in the 19th minute as Lucas Bernardi cleared Eduardo's goalbound header from Mladen Petrić's long free-kick.
Monaco playmaker Camel Meriem tested Pascal Zuberbühler in the 31st minute, and teenager Serge Gakpé was close to scoring on his European debut as the visitors pressed.
[17] After being eliminated from the Champions League in the third qualifying round back in August, Monaco president Michal Pastor had made UEFA Cup success the club's main priority, saying: "We must win it.
The home side had been handed a 21st-minute lead when on-loan striker Christian Vieri converted from the penalty spot after Jaroslav Plašil was brought down by Matías Delgado.
However, Basel took what proved to be the decisive advantage eleven minutes into the second period as Mladen Petrić's cross from the left was headed by Majstorović past Flavio Roma to leave Monaco needing at least two goals for victory.
Just eight minutes had elapsed when Argentinian midfielder Delgado picked himself up after an Edgar Loué foul and curled a superb free-kick around the wall to break the deadlock.
The French team fought back in the second half, before Zdravko Kuzmanovic scored following another Delgado free kick to secure a healthy two-goal lead to take to Stade de la Meinau a week later.
[19] In the Stade de la Meinau in front of just 8,000 spectators, Brazilian striker Eduardo gave the visitors a third-minute advantage, tapping in Mladen Petrić's unselfish square ball.
That lifted Strasbourg and Alexander Farnerud saw three efforts denied, before Eduardo destroyed their hopes with an emphatic volley from David Degen's left-wing cross.
There were still only 26 minutes on the clock and although the game calmed down before half-time, Basel began the second period with renewed verve as Boris Smiljanić and Mile Sterjovski forced impressive saves from Nicolas Puydebois.
On 43 minutes Matías Delgado collected his seventh goal of the competition when his hopeful long-range effort took a wicked bounce off the greasy surface and arced over the unfortunate Mark Schwarzer.
After Eduardo glanced a header wide on ten minutes, he was given a clearer opening when he met Degen's pullback, before testing Schwarzer with a shot on the turn.
Middlesbrough, meanwhile, were limited to half-chances as Jimmy Floyd Hasselbaink drove a free-kick off target midway through the half, while a swerving attempt from Gaizka Mendieta forced Pascal Zuberbühler to tip over.
With opportunities at a premium for Middlesbrough, Basel were rewarded for their endeavour through Delgado's opener, before Degen outpaced a sluggish back line to latch on to Eduardo's through-ball and drill a low shot beyond Schwarzer.
Hasselbaink drew a diving stop from Zuberbühler three minutes into the second period and Chris Riggott went even closer as he met a corner with a towering header.
Christian Gross' Basel always looked in control, having earned a 2-0 victory on home soil during the previous week, and their grip on the tie was further strengthened by Eduardo's close-range finish midway through the first half.
With time almost up, Massimo Maccarone slid in the winning goal from a tight angle to crown a remarkable comeback and earn a last-four tie against Steaua Bucuresti.
The home team came close to halving their deficit in the opening seconds as Pascal Zuberbühler failed to collect George Boateng's high ball under pressure from Yakubu Ayegbeni, but the Nigerian international's angled shot towards the unguarded goal rolled into the side-netting.
That left the home side needing to score four times to stay in the competition, and they replied rapidly as Yakubu's physical presence unsettled the Basel defence and Viduka collected the loose ball before drilling a shot past Zuberbühler.
The Basel goalkeeper preserved his side's two-goal aggregate advantage as the interval approached, however, stretching to palm Yakubu's effort around the post after a slick passing move had sliced open the visitors.
Urged on by tremendous home support Middlesbrough began the second period in frenetic fashion, with half-time substitute Hasselbaink and Viduka both forcing Zuberbühler into action.
Hasselbaink raised home hopes almost immediately with a thunderous shot from the edge of the area and just as it seemed Basel would hold out, Zuberbühler parried Fábio Rochemback's effort and Maccarone slid in the rebound from an acute angle to spark wild celebrations.