The hymnal cites Ezra 18, but there are only 10 chapters in Ezra. Ezekiel 18:30-32 seems to be the intended citation: "30 'Therefore I will judge you, O house of Israel, every one according to his ways, declares the Lord GOD. Repent and turn from all your transgressions, lest iniquity be your ruin. 31 Cast away from you all the transgressions that you have committed, and make yourselves a new heart and a new spirit! Why will you die, O house of Israel? 32 For I have no pleasure in the death of anyone, declares the Lord GOD; so turn, and live.'"
Luke 18:13: "'But the tax collector, standing far off, would not even lift up his eyes to heaven, but beat his breast, saying "God, be merciful to me, a sinner!"'"
Psalm 86:3: "Be gracious to me, O Lord, for to you do I cry all the day."
Job 42:6: "'therefore I despise myself, and repent in dust and ashes.'"
+++
The text is public domain:
Savior, when in dust to Thee
Low we bow the adoring knee;
When, repentant, to the skies
Scarce we lift our weeping eyes;
O, by all Thy pains and woe
Suffered once for us below,
Bending from Thy throne on high,
Hear our penitential cry!
By Thy helpless infant years,
By Thy life of want and tears,
By Thy days of deep distress
In the savage wilderness,
By the dread, mysterious hour
Of the insulting tempter's pow'r,
Turn, O turn a fav'ring eye;
Hear our penitential cry!
By Thine hour of dire despair,
By Thine agony of prayer,
By the cross, the nail, the thorn,
Piercing spear, and torturing scorn,
By the gloom that veiled the skies
O'er the dreadful sacrifice,
Listen to our humble sigh;
Hear our penitential cry!
By Thy deep expiring groan,
By the sad sepulchral stone,
By the vault whose dark abode
Held in vain the rising God,
O, from earth to heav'n restored,
Mighty, reascended Lord,
Bending from Thy throne on high;
Hear our penitential cry!
+++
The cited readings all deal with the call to repentance or the behavior that accompanies repentance, and it's primarily these aspects - rather than specific phrases - that the hymn takes from the cited verses.
The first two lines ("Savior, when in dust to Thee / Low we bow the adoring knee") seem to come from Job's "repent[ing] in dust and ashes," and "When, repentant, to the skies / Scarce we lift our weeping eyes" uses the behavior of the tax collector in Luke 18 as a model.
Each verse ends with "Hear our penitential cry," which has some resemblance to "to you do I cry all the day" from Psalm 86.
The other three verses allude to (among other things) Jesus' temptation in the wilderness (verse two) and events leading up to and including His crucifixion (verse three), death, and resurrection (verse four). Because these events are quickly summarized here, I think it's understandable that they're not listed in the Biblical citations. For the record, though, Jesus' temptation is recounted in Matthew 4:1-11, Mark 1:12-13, and Luke 4:1-13. The other events span too many chapters to be succinctly cited.
