The Cottagers came into their 31st competitive match of season with added impetus after their untimely exit from the Europa League in midweek.
Martin Jol's side squandered a two-goal lead to eventually draw with Odense on Wednesday night, although there was to be no such comeback this afternoon.
Fulham attacked with intent from the offset against the under-pressure Trotters and broke the deadlock in the 32nd minute when Clint Dempsey nodded home Ruiz's cross.
Roles then reversed 66 seconds later when the United States international played through the summer signing, who showed exquisite composure and vision to lift the ball over the onrushing Jussi Jaaskelainen.
Bolton impressed in flashes after the break but were unable to avoid a 13th league defeat of the season as Fulham held out for a seventh clean sheet of the campaign.
Heading into the match, Fulham were hit by the news that Bobby Zamora had failed a late fitness test.
The 30-year-old missed out due to a medial ligament problem in his left knee and was replaced in attack by Andrew Johnson, who was one of seven changes made by Jol after the 2-2 draw with Odense.
Counterpart Owen Coyle, meanwhile, drafted in Marcos Alonso, Fabrice Muamba and Nigel Reo-Coker after Bolton's 2-1 defeat to Aston Villa last weekend.
An edgy start by both sides was encapsulated by an uncharacteristic mistake by Fulham midfielder Dickson Etuhu, who was caught in possession and allowed Reo-Coker to flash a shot across goal.
The effort seemed to spur the west Londoners into life, with Johnson coming close after a neat one-two with Dempsey almost immediately.
Returning skipper Danny Murphy - who fans feared may have aggravated his ankle injury inside five minutes - showed no ill effects shortly after Johnson's effort, seeing a superbly-executed volley deflected just wide.
Johnson had a close-range shot blocked by former Fulham defender Zat Knight as the home side upped the ante, with Etuhu and Brede Hangeland then getting headers away from corners.
Darren Pratley came close with a 20-yard effort during a rare Wanderers attack, before Jaaskelainen turned wide John Arne Riise's drive from 20 yards at the other end.
Bolton were playing like a team devoid of confidence and, after Hangeland twice miscued headers, Dempsey broke the deadlock.
The United States international beat Dedryck Boyata to Ruiz's superb right-wing cross to send home a darted header in the 32nd minute.
Just 66 seconds later, Fulham doubled their advantage thanks to a moment of magic from Ruiz.
The Costa Rica international was put through on goal by Dempsey after outpacing Alonso and, having steadied himself, delightfully scooped the ball over the onrushing Jaaskelainen.
Bolton looked to reduce the deficit as half-time approached, although Ivan Klasnic and Mark Davies were both denied by Fulham's sturdy defence.
Bolton manager Coyle brought on Gretar Steinsson and Chris Eagles, having witnessed a poor first half.
Boyata and Pratley made way but the changes could not stem the Fulham tide as they continued to press for a third.
Bolton captain Kevin Davies made way for David Ngog as a result in the 56th minute, leading to a slightly improved spell from Wanderers.
Klasnic and Muamba were finding good attacking positions, while the visitors were enjoying more possession.
However, Fulham looked dangerous on the break and, after Johnson was adjudged offside when in on goal, Dempsey came agonisingly close to directing home the striker's cross at the back post.
Bolton looked desperate for a goal and, although Eagles and Muamba got efforts away, their exertions left gaping holes at the back.
Johnson and Mousa Dembele almost capitalised as Fulham hunted for a third, which proved elusive as the home side ran out 2-0 victors.