Serie A - Inter leave it late to end winless streak
The Nerazzurri had gone nine games without a win in all competitions prior to this encounter at Stadio Marc Antonio Bentegodi, losing seven, and looked destined for further disappointment when Milito saw a penalty saved and Wesley Sneijder also hit the bar in the first half.
However, with only three minutes remaining Samuel headed home and Milito then nodded in himself with just seconds remaining of normal time to hand Inter a much-needed three points and relieve some of the pressure on coach Claudio Ranieri.
The win takes Inter into sixth place ahead of Roma, who face Palermo on Saturday.
Inter had lost their last five away games without scoring a single goal and wasted a perfect chance to end that drought after 15 minutes. Francesco Acerbi was harshly penalised for handball when the ball bounced up off the turf and against his arm, but Chievo goalkeeper Stefano Sorrentino saved from Milito's spot-kick.
In a first half that offered precious little in the way of real quality, Sneijder - restored to the starting line-up having been benched for the draw against Catania last weekend - produced one fine moment when seeing a curling, dipping effort from 20 yards smack the top of the bar after 19 minutes.
Fellow midfielder Dejan Stankovic was also unfortunate when he teed himself up just outside the box and executed a fierce volley that flew just over the bar. However, Inter were struggling to construct fluent attacking moves and all too often suffered from a lack of quality in the final third.
Chievo threatened even less, although Sergio Pellissier - who has scored five Serie A goals against Inter, second only to his tally against Lazio - did open up the Inter defence just before the break. He controlled expertly from a cross from the right, took a touch to lose Lucio and then saw Julio Cesar block his low effort from an angle.
In first-half injury time, Inter were somewhat unfortunate not to be awarded a second penalty when Sneijder took aim again from the edge of the box but saw his firm effort strike the arm of Paolo Sammarco, only for play to continue despite the protestations of the Dutchman.
He continued to be Inter's most lively participant after the break and almost created a goal after 53 minutes when supplying a delicious cross from the left. However, Andrea Poli just failed to make contact when launching himself at full-stretch at the back post.
Sneijder, who as well as being a direct threat was Inter's chief creator in a rather insipid team performance, then thumped a free kick just wide from 25 yards. Chievo, struggling in front of their home supporters, saw Michael Bradley curl his own free kick just inches over the bar after 80 minutes.
Inter threw on Esteban Cambiasso for the ineffective Poli with six minutes remaining and the Argentina international quickly wasted a glorious chance when he sent his shot high over the bar after Sorrentino had parried a free kick from Sneijder into his path.
However, his countrymen did decide the match in Inter's favour. Samuel was the first to strike with three minutes remaining when he met a cross from the right with a header that floated past Sorrentino and inside the far post.
Milito then added a second on 90 minutes when he met a cross from Zanetti with a firm header from the centre of the penalty area that had Sorrentino easily beaten.
Late it may have been, but Inter's decisive contribution to the tie was vital for a club struggling badly for form on all fronts under Ranieri.
In Serie A's other Friday fixture, Cagliari's Joaquin Larrivey scored a hat-trick but found himself on the losing side as Napoli warmed up for their Champions League fixture at Chelsea with a 6-3 victory at Stadio San Paolo.
The victory, which takes Napoli into joint fourth place with Udinese, was achieved after the home side raced into a three-goal lead thanks to strikes from Marek Hamsik and Paolo Cannavaro and an own goal from Davide Astori.
Larrivey scored the first of his three headers on 37 minutes to pull one back, but Ezequiel Lavezzi scored with a penalty and Walter Gargano finished following some lovely work from Edinson Cavani to make it 5-1 after 70 minutes.
Larrivey converted with two more headers either side of Christian Maggio's low finish as Napoli prevailed in an entertaining contest.