Baker's goal helped TNS win the second leg as the Welsh Premier club set up a tie against Danish side FC Midtjylland.
TNS dominated early on but Cliftonville fought back at Solitude with George McMullan and Ciaran Caldwell hitting the woodwork before half-time.
Ryan Catney struck the TNS bar after the break as the Reds were denied.
The Welsh Premier club started impressively and took an early lead as Baker nodded home a Chris Marriott free-kick.
As the Reds' slow start continued, New Zealand international Greg Draper wasted two glorious chances as he firstly headed straight at Ryan Brown and then nodded wide after a Richie Partridge cross.
However, Cliftonville improved and McMullan struck the woodwork on 27 minutes with a fierce drive with TNS keeper Paul Harrison appearing to get a crucial touch.
As Cliftonville continued to pick up the pace, Martin Donnelly tested Harrison and on the stroke of half-time Caldwell saw a pointblank effort diverted on to a post by the impressive TNS keeper.
The TNS woodwork was rattled again straight after the break as Catney's drive hit the underside of the crossbar before being cleared.
Cliftonville substitute Joe Gormley shot straight at Harrison before heading another glorious chance wide when it seemed easier to score.
As the Reds chased an equaliser, TNS had chances on the break with Brown saving from Craig Jones and Chris Williams having an effort cleared off the line.
Cliftonville continued to press in the closing stages but TNS held on to earn a 2-1 aggregate success.
TEAMS
Cliftonville: Brown, Caldwell, McMullan, Garrett, Martin Donnelly, Smyth, Seydak, McVeigh, Catney, Rory Donnelly, Johnston. Subs: Duffin, Fleming, Chris Scannell, Steele, Templeton, Gormley, Lynch.
The New Saints FC: Harrison, Spender, Marriott, Baker, Evans, Ruscoe, Hogan, Matty Williams, Jones, Draper, Partridge. Subs: Ramsey, Johnson, Sharp, Chris Williams, Seargeant, Darlington, Edwards.
Referee: Magnus Thorisson (Iceland)
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