Saturday's win was only the Kerkrade side's third since Jon Dahl Tomasson took over in January and they go down following NEC's draw with Ajax
Roda, who were fourth bottom when they sacked coach Ruud Brood and replaced him with Jon Dahl Tomasson, started Saturday three points behind NEC and with a better goal difference and needed a victory to stay up but, despite holding up their side of the bargain, champions Ajax were held by the Nijmegen club.
Davy De Beule scored for Roda after 16 minutes and the news from the Amsterdam ArenA was positive with just seven minutes to go.
However, substitute Alireza Jahanbakhsh scored on 74 mintutes to cancel out Jeffrey Leiwakabessy's early own goal but Bojan struck in the 83rd minute to restore the champions' lead, leaving the visitors looking set for automatic relegation.
However, Jahanbakhsh was the hero when he equalised two minutes from time to secure a vital point and condemn Roda to the Eerste Divisie.
NEC have work to do to secure their top-flight status and will contest the relegation play-off with RKC who limped to the end of the season with a 3-0 defeat to Heerenveen with Alfred Finnbogason firing in his 29th goal in 31 games to finish as the league's top scorer.
That ensured NAC Breda were safe regardless of their 2-0 loss at PSV - a result that will see Philipp Cocu's men feature in the Europa League next term.
Twente, having already secured a European berth, earned a 2-2 draw against mid-table PEC Zwolle.
Second-placed Feyenoord were also held to a draw thanks to Johann Gudmundsson's late leveller against AZ, who played their final game under the stewardship of Dick Advocaat before Marco van Basten takes over.
Groningen won a sixth consecutive Eredivisie match for the first time as they beat Heracles 3-1, while ADO Den Haag came from a goal down to see off Cambuur thanks to Michiel Kramer's brace.
Juan Agudelo helped Utrecht to a 2-1 win over Vitesse, who, despite leading the league for a large part of the campaign, will contest the Europa League play-offs along with Heerenveen, Groningen and AZ.